Variant report

Variant	rs1472178
Chromosome Location	chr12:46804175-46804176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46764723..46767273-chr12:46802452..46805727,3	MCF-7	breast:
2	chr12:46798219..46802284-chr12:46803095..46805948,4	K562	blood:
3	chr12:46802430..46804963-chr12:46805880..46807589,2	K562	blood:
4	chr12:46794174..46798124-chr12:46799495..46805327,7	K562	blood:
5	chr12:46804079..46806251-chr12:46809068..46811105,2	K562	blood:
6	chr12:46660899..46662857-chr12:46803892..46806349,2	MCF-7	breast:
7	chr12:46796512..46798026-chr12:46803441..46805172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10748448	0.81[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10748450	0.85[EUR][1000 genomes]
rs10785627	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10785629	0.85[EUR][1000 genomes]
rs1079780	0.81[AMR][1000 genomes]
rs10880966	0.89[AMR][1000 genomes]
rs10880967	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880968	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10880969	0.85[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880970	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10880971	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183484	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11183488	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11183503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183504	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs11183521	1.00[LWK][hapmap]
rs1125909	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11561535	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11837427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12099669	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12298616	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12319162	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12813763	0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs12814341	0.83[AMR][1000 genomes]
rs12816358	0.81[AMR][1000 genomes]
rs12822345	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12832425	0.83[AMR][1000 genomes]
rs12832777	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472179	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492895	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1667	1.00[LWK][hapmap]
rs2045556	0.86[CHB][hapmap]
rs2131371	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[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220727	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2252238	0.93[CHD][hapmap];1.00[LWK][hapmap]
rs2408497	0.88[AMR][1000 genomes]
rs2408498	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3936214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072304	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4076247	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4077708	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[TSI][hapmap];0.85[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768119	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768122	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768123	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[TSI][hapmap];0.84[EUR][1000 genomes]
rs4768696	0.81[AMR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs4768704	0.81[AMR][1000 genomes]
rs4768709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768710	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768711	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768712	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768713	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768714	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768715	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4768716	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[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768717	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768718	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768719	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768724	0.85[EUR][1000 genomes]
rs4768725	0.85[EUR][1000 genomes]
rs4768726	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6582636	0.89[JPT][hapmap]
rs6582641	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582642	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6582643	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582646	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582657	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6582659	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7134289	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7311504	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7312259	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7485580	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486495	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7486532	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7486580	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7487828	0.84[AMR][1000 genomes]
rs7487877	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7488450	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7488577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7489242	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959731	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7968897	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976280	0.82[TSI][hapmap];0.88[AMR][1000 genomes]
rs7980455	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9669404	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9706162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9971879	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
2	chr12:46797000-46819800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:46797800-46805400	Weak transcription	HepG2	liver
4	chr12:46798600-46807200	Weak transcription	Small Intestine	intestine
5	chr12:46798800-46805800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:46798800-46806800	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:46799000-46804400	Weak transcription	NHLF	lung
8	chr12:46799000-46809200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:46800800-46804200	Weak transcription	Psoas Muscle	Psoas
10	chr12:46801000-46808200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:46801200-46805400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:46801800-46804200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:46801800-46805400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:46802000-46804200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:46802000-46812200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:46802200-46805200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:46802600-46804200	Enhancers	HUVEC	blood vessel
18	chr12:46802800-46807200	Weak transcription	Fetal Lung	lung
19	chr12:46803000-46804200	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:46803000-46804200	Weak transcription	Osteobl	bone
21	chr12:46803000-46806800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:46803200-46804200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:46803200-46804200	Weak transcription	Right Atrium	heart
24	chr12:46803200-46804800	Enhancers	Adipose Nuclei	Adipose
25	chr12:46803200-46809400	Weak transcription	Left Ventricle	heart
26	chr12:46803800-46804600	Enhancers	Aorta	Aorta
27	chr12:46803800-46805000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:46804000-46804200	Enhancers	Right Ventricle	heart
29	chr12:46804000-46804800	Flanking Active TSS	Fetal Heart	heart
30	chr12:46804000-46805400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:46804000-46805400	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links