Variant report

Variant	rs472594
Chromosome Location	chr1:228601638-228601639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228600064..228602066-chr1:228619103..228621907,2	K562	blood:
2	chr1:228601250..228603542-chr1:228609261..228610865,3	K562	blood:
3	chr1:228598527..228602511-chr1:228602754..228606216,5	K562	blood:
4	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
5	chr1:228585219..228604537-chr1:228641966..228650471,45	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181218	Chromatin interaction
ENSG00000266174	Chromatin interaction
ENSG00000162931	Chromatin interaction
ENSG00000196890	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158357	0.91[JPT][hapmap]
rs1411912	0.81[YRI][hapmap]
rs1411915	0.93[YRI][hapmap]
rs1888680	0.81[YRI][hapmap]
rs2087121	0.86[JPT][hapmap]
rs4653938	0.91[JPT][hapmap]
rs4653939	0.86[JPT][hapmap]
rs4653942	0.91[JPT][hapmap]
rs493950	0.87[ASW][hapmap];0.84[CHD][hapmap];0.93[YRI][hapmap]
rs494154	0.83[CHB][hapmap]
rs513467	0.87[CHB][hapmap]
rs878388	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
21	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs472594	C1orf96	cis	cerebellum	SCAN
rs472594	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228595600-228602200	Weak transcription	Fetal Intestine Large	intestine
2	chr1:228595600-228602400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:228595600-228603000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:228595600-228603200	Weak transcription	HSMMtube	muscle
5	chr1:228595800-228602400	Weak transcription	Small Intestine	intestine
6	chr1:228595800-228603200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228596000-228601800	Weak transcription	Fetal Thymus	thymus
8	chr1:228596000-228601800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:228596000-228602600	Weak transcription	Left Ventricle	heart
10	chr1:228596000-228602600	Weak transcription	Ovary	ovary
11	chr1:228596000-228603000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:228596000-228603400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:228596200-228603000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:228596200-228603000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:228596200-228603000	Weak transcription	Right Ventricle	heart
16	chr1:228596200-228603400	Weak transcription	NHEK	skin
17	chr1:228596400-228602000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:228596400-228602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:228596400-228602600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:228596400-228602600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:228596400-228602600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:228596400-228603000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:228596400-228603400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:228596400-228603400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:228596400-228603400	Weak transcription	Pancreas	Pancrea
26	chr1:228596400-228615400	Weak transcription	A549	lung
27	chr1:228596600-228603000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:228596600-228603400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:228596600-228603400	Weak transcription	Right Atrium	heart
30	chr1:228596800-228601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:228596800-228602200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:228597000-228603200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:228597400-228603600	Weak transcription	HMEC	breast
34	chr1:228597600-228602800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:228597600-228603000	Weak transcription	Fetal Heart	heart
36	chr1:228598000-228602200	Weak transcription	NHDF-Ad	bronchial
37	chr1:228598200-228602200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:228598400-228602600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:228598400-228603000	Weak transcription	Lung	lung
40	chr1:228598600-228602400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:228598600-228603000	Weak transcription	K562	blood
42	chr1:228598600-228603400	Weak transcription	Gastric	stomach
43	chr1:228598800-228602200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:228598800-228602600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:228598800-228602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:228598800-228603200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:228599000-228602200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:228599000-228602400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:228599000-228603000	Weak transcription	Esophagus	oesophagus
50	chr1:228599000-228603400	Weak transcription	Primary T cells from cord blood	blood

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