Variant report

Variant	rs2476187
Chromosome Location	chr1:62528738-62528739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1013293	0.81[CEU][hapmap]
rs12730782	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs12746804	0.86[ASN][1000 genomes]
rs17379217	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2498978	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2498980	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55725347	0.85[EUR][1000 genomes]
rs6661862	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6668421	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668600	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670849	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6674622	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674784	0.96[EUR][1000 genomes]
rs6681153	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699078	0.87[CHB][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:62495200-62544800	Weak transcription	Liver	Liver
7	chr1:62504800-62531400	Weak transcription	Aorta	Aorta
8	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
9	chr1:62508800-62532000	Weak transcription	Fetal Stomach	stomach
10	chr1:62511400-62531600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:62511400-62531800	Weak transcription	NHEK	skin
12	chr1:62511600-62531200	Weak transcription	Lung	lung
13	chr1:62511800-62529600	Weak transcription	Right Atrium	heart
14	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:62518200-62531600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:62518200-62531800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:62518800-62531600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:62518800-62532000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:62519000-62530600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:62519000-62532000	Weak transcription	Fetal Intestine Large	intestine
21	chr1:62519000-62541600	Weak transcription	HMEC	breast
22	chr1:62519000-62550000	Weak transcription	Primary T cells from cord blood	blood
23	chr1:62519000-62550000	Weak transcription	Pancreas	Pancrea
24	chr1:62519000-62552000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:62520200-62530400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:62521800-62546200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:62523200-62529800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:62523200-62532000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:62523200-62532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:62523200-62533600	Weak transcription	Psoas Muscle	Psoas
31	chr1:62523400-62531000	Weak transcription	Left Ventricle	heart
32	chr1:62524600-62531400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:62524800-62530000	Weak transcription	Fetal Heart	heart
34	chr1:62524800-62530400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:62525000-62532000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:62525600-62529600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:62525600-62530400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:62525800-62530400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:62525800-62530400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:62525800-62531400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:62526400-62530400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:62526600-62532000	Weak transcription	Fetal Intestine Small	intestine
43	chr1:62528400-62529200	ZNF genes & repeats	Fetal Lung	lung
44	chr1:62528400-62530600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:62528600-62531400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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