Variant report

Variant	rs6539269
Chromosome Location	chr12:106840621-106840622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106834815..106838397-chr12:106839925..106842697,3	K562	blood:
2	chr12:106804038..106806221-chr12:106840299..106842123,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10047654	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507211	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10746059	0.80[ASN][1000 genomes]
rs10746060	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778464	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10778465	0.88[ASN][1000 genomes]
rs10778466	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778468	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778469	0.88[ASN][1000 genomes]
rs10778470	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778471	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778473	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778474	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10778475	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778476	0.88[ASN][1000 genomes]
rs10778477	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778478	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778480	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778481	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861571	0.88[CEU][hapmap]
rs10861580	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861581	0.80[ASN][1000 genomes]
rs10861582	0.80[ASN][1000 genomes]
rs10861583	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861585	0.80[ASN][1000 genomes]
rs10861586	0.80[ASN][1000 genomes]
rs10861587	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861588	0.96[CEU][hapmap]
rs10861589	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861590	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861591	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861592	0.88[ASN][1000 genomes]
rs10861593	0.88[ASN][1000 genomes]
rs10861594	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861595	0.88[ASN][1000 genomes]
rs10861597	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861598	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861599	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861601	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861604	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10861605	0.88[ASN][1000 genomes]
rs10861608	0.88[ASN][1000 genomes]
rs10861609	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861613	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112933	0.85[CEU][hapmap]
rs11112940	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs11112942	0.81[ASN][1000 genomes]
rs11112943	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs11112948	0.96[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11112949	0.80[ASN][1000 genomes]
rs11112951	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11112952	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11112953	0.80[ASN][1000 genomes]
rs11112956	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112957	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11112961	0.84[ASN][1000 genomes]
rs11112971	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11112979	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11112980	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11112986	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11112990	0.88[ASN][1000 genomes]
rs11112991	0.88[ASN][1000 genomes]
rs11112992	0.88[ASN][1000 genomes]
rs11112993	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11112995	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113003	0.88[ASN][1000 genomes]
rs11113004	0.88[ASN][1000 genomes]
rs11113009	0.88[ASN][1000 genomes]
rs11113011	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1134577	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs11609315	0.88[ASN][1000 genomes]
rs11611176	0.88[ASN][1000 genomes]
rs11611252	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611815	0.81[ASN][1000 genomes]
rs11615682	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11835357	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835362	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12298876	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305705	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12309708	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309758	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312915	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12322877	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12370430	0.84[CEU][hapmap]
rs12422988	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs12423068	0.88[ASN][1000 genomes]
rs12424952	0.88[CEU][hapmap]
rs12425459	0.88[ASN][1000 genomes]
rs17038414	0.88[ASN][1000 genomes]
rs17218490	0.84[CEU][hapmap]
rs17221107	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17284674	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs1921952	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs2141774	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2141775	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243455	0.81[ASN][1000 genomes]
rs2264759	0.82[AFR][1000 genomes]
rs2374606	0.88[ASN][1000 genomes]
rs2374610	0.84[ASN][1000 genomes]
rs28669886	0.81[ASN][1000 genomes]
rs2888888	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs34955444	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3851631	0.88[ASN][1000 genomes]
rs3851632	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3851633	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4509864	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs55678155	0.88[ASN][1000 genomes]
rs55689816	0.80[ASN][1000 genomes]
rs58297001	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58767490	0.81[ASN][1000 genomes]
rs60224628	0.81[ASN][1000 genomes]
rs60635749	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61940334	0.81[ASN][1000 genomes]
rs61940335	0.81[ASN][1000 genomes]
rs61940342	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61941917	1.00[ASN][1000 genomes]
rs61941918	0.88[ASN][1000 genomes]
rs61941920	0.88[ASN][1000 genomes]
rs61941921	0.88[ASN][1000 genomes]
rs61941922	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941943	0.88[ASN][1000 genomes]
rs61941944	0.88[ASN][1000 genomes]
rs61943672	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61943690	0.88[ASN][1000 genomes]
rs61943693	0.84[ASN][1000 genomes]
rs61943694	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6539268	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6539270	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539271	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67911933	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67966244	0.88[ASN][1000 genomes]
rs7132971	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs7134615	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7134881	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7135054	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7136098	0.84[ASN][1000 genomes]
rs7137445	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139139	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7139249	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297873	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298462	0.80[ASN][1000 genomes]
rs7303873	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7306012	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7306277	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306326	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308541	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7309020	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7310703	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7311957	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313040	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315549	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961133	0.87[CEU][hapmap];0.81[ASN][1000 genomes]
rs7963213	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965520	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969743	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7971581	1.00[ASN][1000 genomes]
rs7976305	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
2	chr12:106787800-106852400	Weak transcription	Gastric	stomach
3	chr12:106787800-106852800	Weak transcription	Pancreas	Pancrea
4	chr12:106802400-106854000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:106812000-106855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:106813000-106864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:106813200-106852800	Weak transcription	HMEC	breast
8	chr12:106813200-106855800	Weak transcription	NHDF-Ad	bronchial
9	chr12:106813200-106864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:106814400-106855800	Weak transcription	Stomach Mucosa	stomach
11	chr12:106819400-106855600	Weak transcription	Right Ventricle	heart
12	chr12:106819600-106845000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:106819600-106846000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:106822000-106852400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:106822000-106853400	Weak transcription	Fetal Brain Female	brain
16	chr12:106822400-106848400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:106823200-106858000	Weak transcription	Psoas Muscle	Psoas
18	chr12:106824800-106866400	Weak transcription	NHLF	lung
19	chr12:106826200-106843600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:106827200-106853000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:106827200-106853200	Weak transcription	Fetal Heart	heart
22	chr12:106828600-106841200	Weak transcription	NH-A	brain
23	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:106828800-106852400	Weak transcription	Fetal Thymus	thymus
25	chr12:106828800-106855800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:106828800-106856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:106829000-106867200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:106829200-106851800	Weak transcription	Fetal Intestine Small	intestine
29	chr12:106830200-106847400	Weak transcription	HUVEC	blood vessel
30	chr12:106830200-106851400	Weak transcription	Spleen	Spleen
31	chr12:106830400-106864600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:106830400-106865800	Weak transcription	K562	blood
33	chr12:106830600-106852400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:106830600-106853000	Weak transcription	HepG2	liver
35	chr12:106830800-106848800	Weak transcription	Aorta	Aorta
36	chr12:106830800-106849400	Weak transcription	HSMMtube	muscle
37	chr12:106831200-106845200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:106831200-106850200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:106831200-106852200	Weak transcription	NHEK	skin
40	chr12:106831200-106856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:106831400-106851600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:106831400-106855200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:106831600-106845600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:106831600-106847200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:106831600-106856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:106831600-106856400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:106831800-106841000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:106832000-106851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:106832800-106841000	Weak transcription	A549	lung
50	chr12:106833000-106849000	Weak transcription	Fetal Lung	lung

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