Variant report

Variant	rs2968887
Chromosome Location	chr12:1262501-1262502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10491955	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs1073938	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1073939	0.83[EUR][1000 genomes]
rs10744533	0.86[CEU][hapmap]
rs10773928	0.87[CEU][hapmap]
rs10773931	0.87[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs10848441	0.86[CEU][hapmap]
rs10848449	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061631	0.81[TSI][hapmap]
rs11061648	0.87[CEU][hapmap]
rs11611107	1.00[JPT][hapmap]
rs11615715	1.00[JPT][hapmap]
rs12300925	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301153	0.81[ASN][1000 genomes]
rs12316126	0.90[GIH][hapmap]
rs12317067	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12322500	0.90[GIH][hapmap]
rs12423086	0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12425157	0.86[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs16928276	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2023941	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369702	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2369703	0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2906107	0.91[ASN][1000 genomes]
rs2906108	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906110	1.00[ASN][1000 genomes]
rs2906113	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968877	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2968884	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968885	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315144	0.87[CEU][hapmap]
rs4372511	0.87[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs56993974	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60297984	0.84[EUR][1000 genomes]
rs60735284	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61911961	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61914293	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61914296	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914297	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914298	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914300	0.83[EUR][1000 genomes]
rs61914303	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914304	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914305	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61914324	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61914326	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61914327	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61914328	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6489269	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs7131703	0.90[GIH][hapmap]
rs7133548	0.84[EUR][1000 genomes]
rs7138610	0.81[ASN][1000 genomes]
rs721859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7316815	0.87[CEU][hapmap]
rs7954247	0.90[GIH][hapmap]
rs7973282	1.00[GIH][hapmap]
rs7973392	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
4	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
18	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
20	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
21	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	nsv1046134	chr12:1153489-1675223	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
24	nsv541344	chr12:1153489-1675223	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
25	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
26	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
27	nsv1039826	chr12:1259831-1483326	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1192800-1280800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:1213000-1266200	Weak transcription	Ovary	ovary
3	chr12:1213600-1277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:1213800-1264400	Weak transcription	Fetal Kidney	kidney
5	chr12:1217600-1277200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:1221800-1277000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:1221800-1277200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:1221800-1283000	Weak transcription	Esophagus	oesophagus
9	chr12:1221800-1301800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:1225400-1292800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:1225600-1280800	Weak transcription	HSMM	muscle
12	chr12:1225600-1280800	Weak transcription	NHDF-Ad	bronchial
13	chr12:1227000-1269200	Weak transcription	Osteobl	bone
14	chr12:1227600-1277200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:1227800-1272000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:1230400-1277200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:1237400-1313800	Weak transcription	Small Intestine	intestine
18	chr12:1239600-1279600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:1239600-1291600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:1239800-1279800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:1240000-1283000	Weak transcription	Right Ventricle	heart
22	chr12:1240200-1272600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:1240200-1291000	Weak transcription	A549	lung
24	chr12:1240600-1262800	Weak transcription	Fetal Intestine Small	intestine
25	chr12:1240600-1271400	Weak transcription	HepG2	liver
26	chr12:1241200-1269400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:1241200-1279600	Weak transcription	Hela-S3	cervix
28	chr12:1241200-1301000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr12:1241200-1306400	Weak transcription	Dnd41	blood
30	chr12:1241200-1307200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:1241400-1307800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:1241600-1270600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:1241800-1279600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:1241800-1292600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:1241800-1326600	Weak transcription	Pancreas	Pancrea
36	chr12:1246600-1262800	Weak transcription	Placenta	Placenta
37	chr12:1246600-1290600	Weak transcription	NHLF	lung
38	chr12:1248000-1265000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:1248000-1283000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:1248200-1262800	Weak transcription	Psoas Muscle	Psoas
41	chr12:1249600-1265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:1249800-1270000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:1251000-1271000	Weak transcription	Brain Germinal Matrix	brain
44	chr12:1251000-1289600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:1252400-1270000	Weak transcription	Colonic Mucosa	Colon
46	chr12:1252600-1280800	Weak transcription	Left Ventricle	heart
47	chr12:1256400-1283200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:1257200-1270400	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:1257800-1270400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:1258400-1299000	Weak transcription	Fetal Muscle Trunk	muscle

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