Variant report

Variant	rs417237
Chromosome Location	chr1:228532195-228532196
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228530715..228532742-chr1:228571055..228573808,2	K562	blood:
2	chr1:228531987..228534463-chr1:228535409..228536944,2	K562	blood:
3	chr1:228527674..228533298-chr1:228643388..228648856,7	K562	blood:
4	chr1:228530911..228533359-chr1:228535027..228537755,2	MCF-7	breast:
5	chr1:228531547..228534494-chr1:228539074..228540724,2	MCF-7	breast:
6	chr1:228532186..228534181-chr1:228558824..228561371,2	K562	blood:
7	chr1:228531850..228533459-chr1:228596981..228599691,2	K562	blood:
8	chr1:228527379..228529811-chr1:228531746..228535149,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270104	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1150912	0.81[CEU][hapmap]
rs287613	0.85[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs35937215	0.93[ASN][1000 genomes]
rs60836537	0.94[ASN][1000 genomes]
rs9726122	0.98[ASN][1000 genomes]
rs9727721	0.98[ASN][1000 genomes]
rs9728020	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv873268	chr1:228442663-228537942	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv873269	chr1:228442663-228543800	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
14	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
15	nsv873272	chr1:228450868-228538968	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv873273	chr1:228450868-228556788	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	nsv873274	chr1:228450868-228585837	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
18	esv1798020	chr1:228456147-228556788	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
19	esv1818776	chr1:228456147-228556788	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	nsv873275	chr1:228456147-228585837	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
21	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
22	nsv873276	chr1:228456943-228585837	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
23	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
24	esv1850422	chr1:228464248-228556788	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
25	nsv468260	chr1:228464248-228556788	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
26	nsv549294	chr1:228464248-228556788	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv873277	chr1:228464248-228556788	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
28	nsv873278	chr1:228464248-228585837	Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
29	nsv468271	chr1:228464248-228601638	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
30	nsv468283	chr1:228464248-228601638	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
31	nsv468294	chr1:228464248-228601638	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
32	nsv549295	chr1:228464248-228601638	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
33	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
34	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
35	nsv873280	chr1:228500627-228603029	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
36	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
37	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
38	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
39	esv3446555	chr1:228529429-228534227	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs417237	RNF187	cis	cerebellum	SCAN
rs417237	C1orf69	cis	cerebellum	SCAN
rs417237	ITPKB	cis	cerebellum	SCAN
rs417237	ACBD3	cis	cerebellum	SCAN
rs417237	MRPL55	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228510000-228554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228511400-228552400	Weak transcription	Psoas Muscle	Psoas
3	chr1:228512400-228532200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:228512800-228532600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:228518800-228534200	Weak transcription	Right Atrium	heart
6	chr1:228520000-228538000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
7	chr1:228520200-228538200	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:228520400-228532400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:228520400-228535000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:228520400-228535200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr1:228522000-228541200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:228527400-228532400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:228527400-228532400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:228527400-228545800	Weak transcription	Fetal Brain Male	brain
15	chr1:228527600-228538600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:228527600-228546600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:228527600-228562400	Weak transcription	Brain Anterior Caudate	brain
18	chr1:228527800-228532200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:228527800-228532400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:228527800-228555800	Weak transcription	Gastric	stomach
21	chr1:228528000-228539200	Weak transcription	Ovary	ovary
22	chr1:228528200-228543400	Weak transcription	HSMMtube	muscle
23	chr1:228528400-228539000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:228528600-228532200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:228529000-228534400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:228529200-228532800	Strong transcription	Primary T cells from cord blood	blood
27	chr1:228529400-228532200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:228529800-228539200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:228530000-228532400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr1:228530000-228536400	Weak transcription	Fetal Intestine Large	intestine
31	chr1:228530000-228547200	Weak transcription	Pancreas	Pancrea
32	chr1:228530400-228532800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:228530400-228533000	Strong transcription	Fetal Intestine Small	intestine
34	chr1:228531000-228532200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:228531000-228532200	Weak transcription	Placenta	Placenta
36	chr1:228531000-228538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:228531200-228532200	Weak transcription	Lung	lung
38	chr1:228531200-228532200	ZNF genes & repeats	Hela-S3	cervix
39	chr1:228531200-228549600	Weak transcription	Esophagus	oesophagus
40	chr1:228531200-228551200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:228531400-228532200	Strong transcription	Brain Cingulate Gyrus	brain
42	chr1:228531400-228532200	ZNF genes & repeats	Fetal Kidney	kidney
43	chr1:228531400-228532200	Strong transcription	Dnd41	blood
44	chr1:228531400-228532400	Strong transcription	Fetal Lung	lung
45	chr1:228531400-228532400	Weak transcription	Right Ventricle	heart
46	chr1:228531400-228532800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr1:228531400-228532800	ZNF genes & repeats	A549	lung
48	chr1:228531600-228532400	Weak transcription	Fetal Stomach	stomach
49	chr1:228531600-228538600	Weak transcription	Brain Germinal Matrix	brain
50	chr1:228531800-228532200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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