Variant report

Variant	rs829620
Chromosome Location	chr2:30750660-30750661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30745608..30747165-chr2:30749451..30751704,2	K562	blood:
2	chr2:30740997..30743225-chr2:30749540..30752188,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10167083	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183928	0.85[JPT][hapmap]
rs12052260	0.82[YRI][hapmap]
rs12053428	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1252625	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1252631	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252651	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1447193	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1525062	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1869423	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1869424	0.86[CEU][hapmap]
rs1975555	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2121600	0.81[CEU][hapmap]
rs2123753	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2177698	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2593457	0.83[EUR][1000 genomes]
rs2593474	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2602767	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2602808	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2609917	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2609945	0.82[JPT][hapmap]
rs2609951	0.82[EUR][1000 genomes]
rs2609954	0.82[EUR][1000 genomes]
rs2609960	0.81[EUR][1000 genomes]
rs2692035	0.89[EUR][1000 genomes]
rs4952147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731031	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs6740440	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs6749074	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7583211	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.82[JPT][hapmap]
rs829564	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829574	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs829575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829578	0.85[EUR][1000 genomes]
rs829582	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs829583	0.89[EUR][1000 genomes]
rs829618	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829622	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829630	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829632	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829641	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs829653	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829654	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829662	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829663	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829664	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs829665	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs829669	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs829670	0.87[EUR][1000 genomes]
rs829671	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs829672	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs829675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829677	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829679	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs829681	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829682	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs829695	0.85[JPT][hapmap]
rs829696	0.85[JPT][hapmap]
rs829699	0.85[JPT][hapmap]
rs844194	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860487	1.00[JPT][hapmap]
rs866680	0.85[JPT][hapmap]
rs9309680	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:30733000-30756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:30736800-30752400	Weak transcription	Psoas Muscle	Psoas
5	chr2:30738000-30757000	Weak transcription	Ovary	ovary
6	chr2:30738200-30750800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:30738200-30750800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:30738200-30751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:30738200-30752400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:30738200-30758200	Weak transcription	Right Ventricle	heart
11	chr2:30738400-30756200	Weak transcription	Hela-S3	cervix
12	chr2:30743000-30752200	Weak transcription	HSMMtube	muscle
13	chr2:30743000-30754800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:30743000-30756000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:30743000-30756000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:30743000-30756000	Weak transcription	HepG2	liver
17	chr2:30743000-30757000	Weak transcription	Left Ventricle	heart
18	chr2:30743000-30758200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:30743000-30758200	Weak transcription	Pancreas	Pancrea
20	chr2:30743000-30758400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:30743000-30758600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:30743000-30759000	Weak transcription	Gastric	stomach
23	chr2:30743000-30759800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:30743000-30759800	Weak transcription	Esophagus	oesophagus
25	chr2:30743000-30761000	Weak transcription	NHEK	skin
26	chr2:30743000-30763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:30743000-30764600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:30743000-30764600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:30743000-30767400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:30743000-30768000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:30743200-30750800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:30743200-30750800	Weak transcription	Spleen	Spleen
33	chr2:30743200-30752200	Weak transcription	Aorta	Aorta
34	chr2:30743200-30755800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:30743200-30755800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:30743200-30756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:30743200-30756000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:30743200-30756000	Weak transcription	Fetal Intestine Large	intestine
39	chr2:30743200-30757000	Weak transcription	Fetal Stomach	stomach
40	chr2:30743200-30757000	Weak transcription	Lung	lung
41	chr2:30743200-30757400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:30743200-30760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:30743600-30756000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:30743600-30756200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:30744000-30756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:30744000-30756000	Weak transcription	Fetal Thymus	thymus
47	chr2:30744000-30756200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:30746000-30750800	Weak transcription	NHDF-Ad	bronchial
49	chr2:30746000-30757600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:30746400-30754600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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