Variant report

Variant	rs3782188
Chromosome Location	chr12:25249545-25249546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:25248821-25249951	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000258546	TF binding region
LRMP	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10743538	0.91[ASN][1000 genomes]
rs10842462	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10842507	0.92[CEU][hapmap]
rs10842508	0.85[CHB][hapmap]
rs11047821	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11047826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047837	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11047842	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11047845	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11047857	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11047880	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11047882	0.85[CHB][hapmap]
rs11047892	0.92[CEU][hapmap]
rs11047918	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11531007	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11533487	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs12228277	0.85[CEU][hapmap]
rs12228408	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12229161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229450	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12230737	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs12423047	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12423489	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs12423778	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426684	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12427119	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12427141	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs12427150	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17329424	0.85[CEU][hapmap]
rs17387444	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291364	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2970532	0.85[CEU][hapmap]
rs3924649	0.85[CHB][hapmap]
rs4441109	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs4623993	0.85[CHB][hapmap]
rs4963852	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4963853	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56024196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069103	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73069105	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73071272	0.82[EUR][1000 genomes]
rs73077316	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73077322	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73079611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73079683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73081704	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7312175	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs7969931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7973746	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs7973851	0.92[ASN][1000 genomes]
rs7979296	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2757492	chr12:25233781-25252178	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2759884	chr12:25233781-25252178	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25212000-25250800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:25227400-25251000	Weak transcription	Pancreas	Pancrea
7	chr12:25229000-25253000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
9	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:25238600-25251000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
12	chr12:25238600-25265200	Weak transcription	Lung	lung
13	chr12:25238800-25251000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:25239800-25253200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:25240000-25251000	Weak transcription	Spleen	Spleen
16	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:25243200-25250800	Weak transcription	Liver	Liver
19	chr12:25246400-25252600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:25246400-25264000	Weak transcription	Ovary	ovary
21	chr12:25247400-25253000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
23	chr12:25247600-25251000	Weak transcription	Adipose Nuclei	Adipose
24	chr12:25247800-25258000	Strong transcription	Primary B cells from cord blood	blood
25	chr12:25248000-25253000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:25248600-25252600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:25248600-25257800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:25248800-25249800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:25248800-25251400	Strong transcription	GM12878-XiMat	blood
33	chr12:25248800-25255800	Strong transcription	Thymus	Thymus
34	chr12:25248800-25258000	Strong transcription	Dnd41	blood
35	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:25249000-25249800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:25249000-25252200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:25249400-25250000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:25249400-25250000	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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