Variant report

Variant	rs2369701
Chromosome Location	chr12:1259831-1259832
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10848438	0.87[CHB][hapmap]
rs10848442	0.93[CHB][hapmap]
rs12426509	0.80[CEU][hapmap];0.81[CHD][hapmap]
rs1544425	0.81[CEU][hapmap]
rs16928347	0.82[JPT][hapmap]
rs17223448	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs17800876	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs1859449	0.83[EUR][1000 genomes]
rs2189788	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2286037	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2906103	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2906105	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2906106	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2906109	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2906111	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2906112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2968869	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2968874	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968875	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968876	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968880	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968881	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968882	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2968899	0.93[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs3924361	0.93[CHB][hapmap]
rs4439574	0.80[EUR][1000 genomes]
rs4511332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs6489270	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7137058	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7137563	0.87[CEU][hapmap]
rs7299878	0.84[CEU][hapmap]
rs7303850	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap]
rs7310001	0.84[JPT][hapmap]
rs7311531	0.88[CEU][hapmap]
rs7954213	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs7971670	0.84[CEU][hapmap];0.81[CHD][hapmap]
rs7980065	0.82[CHB][hapmap]
rs9943709	0.81[EUR][1000 genomes]
rs9943818	0.82[JPT][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2369701	DDX28	trans	parietal	SCAN
rs2369701	NRIP2	cis	cerebellum	SCAN

Chromatin state (count:96 , 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	chr12:1206800-1260600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:1209800-1261600	Weak transcription	Aorta	Aorta
4	chr12:1213000-1266200	Weak transcription	Ovary	ovary
5	chr12:1213600-1277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:1213800-1264400	Weak transcription	Fetal Kidney	kidney
7	chr12:1217600-1277200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:1221400-1260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:1221600-1261800	Weak transcription	Fetal Stomach	stomach
10	chr12:1221800-1260800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:1221800-1277000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:1221800-1277200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:1221800-1283000	Weak transcription	Esophagus	oesophagus
14	chr12:1221800-1301800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:1225200-1260600	Weak transcription	HSMMtube	muscle
16	chr12:1225400-1261600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:1225400-1261600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:1225400-1292800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:1225600-1260600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr12:1225600-1280800	Weak transcription	HSMM	muscle
21	chr12:1225600-1280800	Weak transcription	NHDF-Ad	bronchial
22	chr12:1227000-1269200	Weak transcription	Osteobl	bone
23	chr12:1227600-1277200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:1227800-1272000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:1230400-1277200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:1230800-1260600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:1232400-1261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:1237200-1261800	Weak transcription	HMEC	breast
29	chr12:1237400-1313800	Weak transcription	Small Intestine	intestine
30	chr12:1239600-1260000	Weak transcription	Fetal Lung	lung
31	chr12:1239600-1261600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:1239600-1279600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:1239600-1291600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:1239800-1261600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:1239800-1279800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:1240000-1261400	Weak transcription	Thymus	Thymus
37	chr12:1240000-1283000	Weak transcription	Right Ventricle	heart
38	chr12:1240200-1272600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:1240200-1291000	Weak transcription	A549	lung
40	chr12:1240600-1262800	Weak transcription	Fetal Intestine Small	intestine
41	chr12:1240600-1271400	Weak transcription	HepG2	liver
42	chr12:1240800-1260600	Weak transcription	Fetal Intestine Large	intestine
43	chr12:1241200-1269400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:1241200-1279600	Weak transcription	Hela-S3	cervix
45	chr12:1241200-1301000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:1241200-1306400	Weak transcription	Dnd41	blood
47	chr12:1241200-1307200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:1241400-1262400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:1241400-1307800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr12:1241600-1270600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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