Variant report

Variant	rs2476180
Chromosome Location	chr1:62517703-62517704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11576777	1.00[JPT][hapmap]
rs11577828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585888	1.00[JPT][hapmap]
rs11590485	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332631	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1363	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17122938	1.00[CHB][hapmap]
rs17122997	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs17123017	1.00[CHB][hapmap]
rs17313395	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2067881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2067882	1.00[CHB][hapmap]
rs2365985	1.00[CHB][hapmap]
rs3762449	1.00[CHB][hapmap]
rs41394744	1.00[CHB][hapmap]
rs4325166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915603	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915795	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56379320	0.93[ASN][1000 genomes]
rs61777663	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61777664	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61777665	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61777666	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661849	1.00[JPT][hapmap]
rs6673889	1.00[JPT][hapmap]
rs6685442	1.00[JPT][hapmap]
rs6697273	1.00[CHB][hapmap]
rs7519802	1.00[JPT][hapmap]
rs7528431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7537406	0.83[EUR][1000 genomes]
rs7537873	0.82[EUR][1000 genomes]
rs7539653	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
2	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:62474200-62518600	Weak transcription	Primary T cells from cord blood	blood
8	chr1:62484400-62523000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:62488400-62521200	Weak transcription	Ovary	ovary
11	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
13	chr1:62495200-62544800	Weak transcription	Liver	Liver
14	chr1:62502200-62520600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:62503600-62520200	Weak transcription	Fetal Brain Male	brain
16	chr1:62504800-62531400	Weak transcription	Aorta	Aorta
17	chr1:62507200-62523000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:62507200-62523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:62507400-62524600	Weak transcription	HepG2	liver
20	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
21	chr1:62508800-62532000	Weak transcription	Fetal Stomach	stomach
22	chr1:62511400-62531600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:62511400-62531800	Weak transcription	NHEK	skin
24	chr1:62511600-62518800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:62511600-62520000	Weak transcription	Right Ventricle	heart
26	chr1:62511600-62522600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:62511600-62522800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:62511600-62531200	Weak transcription	Lung	lung
29	chr1:62511800-62521600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:62511800-62522600	Weak transcription	Psoas Muscle	Psoas
31	chr1:62511800-62523200	Weak transcription	Fetal Heart	heart
32	chr1:62511800-62529600	Weak transcription	Right Atrium	heart
33	chr1:62512200-62524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:62512400-62518800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:62513600-62518800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:62514000-62522800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:62514000-62522800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:62514000-62522800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:62514000-62524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:62515200-62523200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:62515400-62519000	Strong transcription	Fetal Intestine Large	intestine
42	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:62515800-62522600	Weak transcription	Left Ventricle	heart
44	chr1:62516000-62518200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:62516000-62518800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:62516000-62519200	Weak transcription	Brain Germinal Matrix	brain
47	chr1:62516000-62519600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:62516200-62519000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:62516200-62519800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:62516400-62519000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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