Variant report

Variant	rs12315996
Chromosome Location	chr12:49887733-49887734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49760922..49762570-chr12:49885897..49888563,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10160947	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506285	1.00[JPT][hapmap]
rs10783314	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10875948	1.00[CHB][hapmap]
rs10875958	0.82[EUR][1000 genomes]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11168988	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169005	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169008	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169009	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169014	0.84[EUR][1000 genomes]
rs11169015	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11169016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11169017	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11169027	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169043	0.84[EUR][1000 genomes]
rs11169045	0.83[EUR][1000 genomes]
rs11169048	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169049	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169058	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169059	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169063	0.83[ASW][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap]
rs11611743	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11615710	0.81[EUR][1000 genomes]
rs11830144	1.00[CHD][hapmap]
rs11834161	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11835037	1.00[CHB][hapmap]
rs11837234	1.00[CHB][hapmap]
rs12296440	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299282	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12300817	1.00[ASN][1000 genomes]
rs12301632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12305716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12306212	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12306645	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12310129	1.00[JPT][hapmap]
rs12314428	1.00[ASN][1000 genomes]
rs12316170	1.00[ASN][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12318633	1.00[ASN][1000 genomes]
rs12320284	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12322571	1.00[ASN][1000 genomes]
rs12581343	1.00[CHB][hapmap]
rs12581428	1.00[CHB][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123764	1.00[CHD][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123865	1.00[CHB][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2236746	1.00[CHB][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4641552	1.00[CHD][hapmap]
rs57200170	1.00[ASN][1000 genomes]
rs57601151	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58095611	0.82[EUR][1000 genomes]
rs60808917	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6580711	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580715	0.83[EUR][1000 genomes]
rs6580716	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7132684	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7133398	0.85[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap]
rs7139061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7294648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294973	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295162	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7295247	1.00[CHB][hapmap]
rs7295556	0.93[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73297209	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73301240	1.00[ASN][1000 genomes]
rs73301259	1.00[ASN][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342365	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7342384	1.00[CHB][hapmap]
rs7488923	0.86[EUR][1000 genomes]
rs7955541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7962951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7963954	0.84[GIH][hapmap]
rs7965658	0.87[GIH][hapmap]
rs7969010	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7969099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7970059	0.85[EUR][1000 genomes]
rs7974420	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7975712	0.83[ASW][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs7976165	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7979285	0.81[YRI][hapmap]
rs7980731	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs9919739	0.83[ASN][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9919807	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS 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	39 gene(s)	inside rSNPs	diseases
6	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
3	chr12:49850400-49911000	Weak transcription	K562	blood
4	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
5	chr12:49856600-49890200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:49856600-49890200	Weak transcription	Ovary	ovary
7	chr12:49856800-49898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:49859400-49888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:49869600-49890000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:49872200-49895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:49873000-49890400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:49873800-49904600	Weak transcription	Fetal Heart	heart
16	chr12:49874000-49889800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:49874000-49904400	Weak transcription	Fetal Brain Male	brain
18	chr12:49874200-49890600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:49874800-49914200	Weak transcription	Fetal Kidney	kidney
20	chr12:49876400-49894800	Weak transcription	Fetal Intestine Large	intestine
21	chr12:49876400-49897600	Weak transcription	Small Intestine	intestine
22	chr12:49876400-49911200	Weak transcription	Adipose Nuclei	Adipose
23	chr12:49876600-49890000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:49876600-49893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:49876800-49888400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:49876800-49890000	Weak transcription	NHLF	lung
27	chr12:49876800-49890200	Weak transcription	Fetal Thymus	thymus
28	chr12:49876800-49890400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:49876800-49898000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:49876800-49905200	Weak transcription	Right Ventricle	heart
31	chr12:49876800-49916200	Weak transcription	Psoas Muscle	Psoas
32	chr12:49877000-49893000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:49877000-49908800	Weak transcription	NHDF-Ad	bronchial
34	chr12:49877000-49909000	Weak transcription	Brain Germinal Matrix	brain
35	chr12:49877600-49902000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49877800-49889600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:49878000-49893600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:49878200-49892400	Weak transcription	Liver	Liver
39	chr12:49878600-49890200	Weak transcription	Brain Angular Gyrus	brain
40	chr12:49878600-49918600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr12:49879600-49890000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:49880200-49893200	Weak transcription	Fetal Lung	lung
43	chr12:49880400-49888400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:49880400-49890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:49880400-49916000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:49881000-49892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:49881400-49888600	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:49881600-49888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:49881800-49888600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:49881800-49890000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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