Variant report

Variant	rs12999675
Chromosome Location	chr2:64136069-64136070
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10166971	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175674	0.89[CHB][hapmap]
rs12463827	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12466966	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12468093	0.84[EUR][1000 genomes]
rs12474366	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12475294	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12988017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990604	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12993544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997303	0.85[EUR][1000 genomes]
rs13005218	0.85[EUR][1000 genomes]
rs13007342	0.85[EUR][1000 genomes]
rs13007731	0.85[EUR][1000 genomes]
rs13009774	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13010817	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13014781	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13023542	0.90[EUR][1000 genomes]
rs13025640	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13028805	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034260	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345479	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437455	0.86[EUR][1000 genomes]
rs1545196	0.85[EUR][1000 genomes]
rs17555655	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17562312	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17620012	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701685	0.87[EUR][1000 genomes]
rs17701709	0.87[EUR][1000 genomes]
rs17752683	0.86[EUR][1000 genomes]
rs2287361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422110	0.81[EUR][1000 genomes]
rs34043307	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34145077	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34196086	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34200806	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34239752	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34512058	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34900788	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35058898	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35122209	0.85[EUR][1000 genomes]
rs35247801	0.85[EUR][1000 genomes]
rs35253921	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35521527	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35552326	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35648996	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35810427	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35972278	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35975566	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36099158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815616	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3934536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4075010	0.88[EUR][1000 genomes]
rs4482470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4544421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4599090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671534	0.93[ASN][1000 genomes]
rs4671535	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[ASN][1000 genomes]
rs4671537	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671538	0.86[EUR][1000 genomes]
rs66476638	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66535980	0.87[EUR][1000 genomes]
rs66595136	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66650505	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66660401	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66993685	0.86[EUR][1000 genomes]
rs6730664	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67366434	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67962955	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71422402	0.84[EUR][1000 genomes]
rs72808216	0.90[EUR][1000 genomes]
rs72808218	0.87[EUR][1000 genomes]
rs72808231	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808236	0.86[ASN][1000 genomes]
rs72808248	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72808254	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72808262	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72808287	0.85[EUR][1000 genomes]
rs874695	0.84[EUR][1000 genomes]
rs893779	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.82[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	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
2	chr2:64114200-64174800	Weak transcription	Right Ventricle	heart
3	chr2:64116800-64138600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:64118200-64153600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:64118400-64137800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:64119600-64139600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:64126000-64138000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:64126200-64138800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:64127200-64138000	Weak transcription	HSMMtube	muscle
10	chr2:64127400-64138600	Weak transcription	Psoas Muscle	Psoas
11	chr2:64129200-64138000	Weak transcription	Left Ventricle	heart
12	chr2:64129600-64138200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:64129600-64138200	Weak transcription	NH-A	brain
14	chr2:64129600-64139000	Weak transcription	Spleen	Spleen
15	chr2:64129600-64153200	Weak transcription	Thymus	Thymus
16	chr2:64129600-64153600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:64129600-64153600	Weak transcription	Aorta	Aorta
18	chr2:64129600-64153600	Weak transcription	Pancreas	Pancrea
19	chr2:64129600-64154000	Weak transcription	Colonic Mucosa	Colon
20	chr2:64129600-64164000	Weak transcription	NHLF	lung
21	chr2:64129600-64201000	Weak transcription	Hela-S3	cervix
22	chr2:64129800-64154200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:64130000-64138000	Weak transcription	Lung	lung
24	chr2:64130000-64153200	Weak transcription	Gastric	stomach
25	chr2:64130000-64153600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:64130000-64153800	Weak transcription	Esophagus	oesophagus
27	chr2:64130200-64137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:64130200-64138200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:64130200-64149200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:64130200-64153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:64130200-64153600	Weak transcription	Fetal Intestine Small	intestine
32	chr2:64130200-64153600	Weak transcription	Ovary	ovary
33	chr2:64130200-64153800	Weak transcription	Fetal Stomach	stomach
34	chr2:64130400-64137000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:64130400-64138400	Weak transcription	NHDF-Ad	bronchial
36	chr2:64130400-64138800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:64130400-64144400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:64130400-64155000	Strong transcription	HepG2	liver
39	chr2:64130400-64167600	Weak transcription	Fetal Heart	heart
40	chr2:64130400-64168400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:64130400-64211200	Weak transcription	Fetal Brain Male	brain
42	chr2:64130600-64137800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:64130600-64138000	Weak transcription	HUVEC	blood vessel
44	chr2:64130600-64140800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:64130600-64144400	Weak transcription	HMEC	breast
46	chr2:64130600-64153600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:64130600-64168000	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:64130800-64137200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:64130800-64138000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:64130800-64174800	Weak transcription	Stomach Mucosa	stomach

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