Variant report

Variant	rs2884629
Chromosome Location	chr1:197552034-197552035
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10737693	0.94[ASN][1000 genomes]
rs10801605	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10922215	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10922216	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs10922221	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10922223	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10922225	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs10922249	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11583319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11588864	0.88[ASN][1000 genomes]
rs11799515	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11799915	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11802794	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12092948	0.88[ASN][1000 genomes]
rs12117045	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12118913	0.84[ASN][1000 genomes]
rs12131588	0.87[ASN][1000 genomes]
rs12141028	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs12142127	1.00[CEU][hapmap]
rs12354257	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12724239	0.91[ASN][1000 genomes]
rs12748009	0.91[ASN][1000 genomes]
rs1421399	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539414	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1573100	0.86[ASN][1000 genomes]
rs16841842	0.92[ASN][1000 genomes]
rs16841904	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs16841912	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs17564924	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17621130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1775448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1775452	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476020	0.88[JPT][hapmap]
rs2477059	0.86[ASN][1000 genomes]
rs2477073	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477077	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2488389	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2488393	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2488397	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2488398	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2488401	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2494268	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs2759662	0.88[JPT][hapmap]
rs2759663	0.88[JPT][hapmap]
rs2821102	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs2821121	0.88[JPT][hapmap]
rs35939830	1.00[ASN][1000 genomes]
rs4316387	0.88[ASN][1000 genomes]
rs6702421	1.00[ASN][1000 genomes]
rs7522325	0.80[CEU][hapmap];0.86[CHB][hapmap];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	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3397065	chr1:197545083-197637033	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197506800-197564600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:197508400-197602400	Weak transcription	Left Ventricle	heart
3	chr1:197526800-197563000	Weak transcription	Osteobl	bone
4	chr1:197537000-197574600	Weak transcription	NHDF-Ad	bronchial
5	chr1:197537400-197602200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:197537800-197585600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:197538000-197554000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:197538600-197563600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:197539000-197554400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:197539000-197556600	Weak transcription	Fetal Kidney	kidney
11	chr1:197540000-197554600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:197541800-197566000	Weak transcription	Ovary	ovary
13	chr1:197541800-197602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:197541800-197602600	Weak transcription	Fetal Thymus	thymus
15	chr1:197542000-197552200	Weak transcription	Primary T cells from cord blood	blood
16	chr1:197542000-197554000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:197542000-197555800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:197542000-197557000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:197542000-197559600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:197542000-197559800	Weak transcription	Liver	Liver
21	chr1:197542000-197568000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:197542000-197569200	Weak transcription	Pancreas	Pancrea
23	chr1:197542000-197571400	Weak transcription	Esophagus	oesophagus
24	chr1:197542000-197574400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:197542000-197609000	Weak transcription	Colonic Mucosa	Colon
26	chr1:197542000-197626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:197542600-197563200	Weak transcription	Fetal Heart	heart
28	chr1:197544000-197553600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:197544000-197562000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:197544400-197602400	Weak transcription	Primary B cells from cord blood	blood
31	chr1:197544600-197570000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:197545400-197552600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:197545600-197553200	Strong transcription	Dnd41	blood
34	chr1:197545600-197567400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:197547000-197587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:197547400-197602400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:197547600-197566200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:197548600-197553200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:197548600-197569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:197550400-197552600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:197550400-197552600	Strong transcription	Fetal Lung	lung
42	chr1:197550400-197553000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:197550400-197553200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:197550600-197556800	Weak transcription	HMEC	breast
45	chr1:197550800-197555200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:197551000-197552600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:197551400-197585600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:197551800-197552600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:197551800-197559400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:197552000-197553000	Strong transcription	Primary T cells fromperipheralblood	blood

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