Variant report

Variant	rs4396117
Chromosome Location	chr1:228429583-228429584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228426928..228429804-chr1:228442378..228444505,2	MCF-7	breast:
2	chr1:228423250..228427133-chr1:228428508..228431857,5	K562	blood:
3	chr1:228427134..228429598-chr1:228591173..228592748,2	K562	blood:

Variant related genes	Relation type
ENSG00000154358	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10916309	1.00[EUR][1000 genomes]
rs10916310	1.00[EUR][1000 genomes]
rs10916312	1.00[EUR][1000 genomes]
rs11804099	1.00[EUR][1000 genomes]
rs11808955	1.00[EUR][1000 genomes]
rs1188486	1.00[EUR][1000 genomes]
rs12073379	1.00[EUR][1000 genomes]
rs12084050	1.00[EUR][1000 genomes]
rs12090413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12092786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093044	1.00[EUR][1000 genomes]
rs12095133	1.00[EUR][1000 genomes]
rs16848604	1.00[EUR][1000 genomes]
rs2087120	1.00[EUR][1000 genomes]
rs473316	1.00[EUR][1000 genomes]
rs477699	1.00[EUR][1000 genomes]
rs56690462	1.00[EUR][1000 genomes]
rs56757399	1.00[EUR][1000 genomes]
rs58670384	1.00[EUR][1000 genomes]
rs59958468	1.00[EUR][1000 genomes]
rs61149796	1.00[EUR][1000 genomes]
rs61416971	1.00[EUR][1000 genomes]
rs73099694	1.00[EUR][1000 genomes]
rs73101117	1.00[EUR][1000 genomes]
rs74140903	1.00[EUR][1000 genomes]
rs74142661	1.00[EUR][1000 genomes]
rs74142677	1.00[EUR][1000 genomes]
rs7513176	1.00[EUR][1000 genomes]
rs827827	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	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
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228414400-228430400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:228417200-228433000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:228418400-228436000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:228419600-228429600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:228422200-228434800	ZNF genes & repeats	Dnd41	blood
6	chr1:228422400-228431000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
7	chr1:228423600-228429800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:228424400-228429600	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr1:228424400-228430800	Strong transcription	Left Ventricle	heart
10	chr1:228425800-228434200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:228426000-228435200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr1:228426400-228429800	Strong transcription	Right Ventricle	heart
13	chr1:228426400-228430000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:228426600-228434400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:228426800-228429800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:228427000-228430200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:228427000-228435600	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr1:228427200-228430800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:228427200-228434600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:228427400-228432000	Weak transcription	Psoas Muscle	Psoas
21	chr1:228428000-228429600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
22	chr1:228428000-228432200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:228428000-228433400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr1:228428200-228430800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
25	chr1:228428200-228433200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr1:228428200-228434200	ZNF genes & repeats	Fetal Lung	lung
27	chr1:228428200-228434600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:228428200-228435000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr1:228428400-228429800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:228428400-228434000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr1:228428400-228434400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr1:228428400-228434600	ZNF genes & repeats	Liver	Liver
33	chr1:228428400-228434600	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr1:228428400-228435200	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr1:228428400-228436600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr1:228428600-228431000	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr1:228428600-228433600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:228428600-228434400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr1:228428600-228434600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
40	chr1:228428600-228434800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
41	chr1:228428600-228435000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr1:228428600-228435000	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr1:228428800-228430200	Weak transcription	Hela-S3	cervix
44	chr1:228428800-228430400	Weak transcription	A549	lung
45	chr1:228428800-228430800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:228428800-228431400	ZNF genes & repeats	Brain Anterior Caudate	brain
47	chr1:228428800-228434800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr1:228429000-228431200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:228429000-228434800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle

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