Variant report

Variant	rs17118431
Chromosome Location	chr12:56667100-56667101
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	chr12:56667048-56667460	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:56666963-56667263	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56666983-56667410	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56659385..56662814-chr12:56663155..56667840,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258260	TF binding region
ENSG00000135469	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10876882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11171803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11171806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11575224	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11575229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11575232	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11575248	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1274490	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1274496	0.81[EUR][1000 genomes]
rs1295772	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118403	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1802236	0.81[AMR][1000 genomes]
rs2020854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap]
rs2066807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2066819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306693	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[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2371454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2629447	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2629452	0.86[EUR][1000 genomes]
rs2643626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2695782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2695788	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2695789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35526714	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41363748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs41392645	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[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41423244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57137641	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57279772	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57343616	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57870697	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58852079	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59295315	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59626664	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59822547	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60192809	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60542959	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60913149	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs744051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773664	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs808919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17118431	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs17118431	RP11-977G19.11	cis	Artery Aorta	GTEx
rs17118431	RP11-977G19.11	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56661400-56684400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:56661600-56669600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56661600-56671600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:56661800-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56661800-56667200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:56661800-56667200	Weak transcription	Fetal Lung	lung
7	chr12:56661800-56667200	Weak transcription	Small Intestine	intestine
8	chr12:56661800-56668200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:56662000-56690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:56662200-56678200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56662400-56670600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:56662400-56673200	Strong transcription	HSMM	muscle
13	chr12:56662400-56677200	Strong transcription	Primary T cells from cord blood	blood
14	chr12:56662400-56680800	Strong transcription	Brain Hippocampus Middle	brain
15	chr12:56662400-56692400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:56662600-56673400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:56662600-56680800	Strong transcription	Placenta	Placenta
18	chr12:56662600-56681000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:56662600-56681000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:56662600-56681400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:56662600-56682800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:56662600-56685400	Strong transcription	Fetal Thymus	thymus
23	chr12:56662600-56686000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:56662600-56690000	Strong transcription	Fetal Muscle Leg	muscle
25	chr12:56662800-56667800	Genic enhancers	Liver	Liver
26	chr12:56662800-56670200	Strong transcription	Brain Anterior Caudate	brain
27	chr12:56662800-56670600	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr12:56662800-56679600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:56662800-56680000	Strong transcription	Lung	lung
30	chr12:56662800-56680600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56662800-56680800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:56662800-56680800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:56662800-56680800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:56662800-56680800	Strong transcription	Thymus	Thymus
35	chr12:56662800-56681000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:56662800-56681000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:56662800-56682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:56662800-56682200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:56662800-56682800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:56662800-56683200	Strong transcription	Dnd41	blood
41	chr12:56662800-56686400	Strong transcription	Fetal Stomach	stomach
42	chr12:56663000-56670200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:56663000-56680600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:56663000-56680600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:56663000-56692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:56663200-56668800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:56663200-56678000	Strong transcription	NHLF	lung
48	chr12:56663200-56680400	Strong transcription	Osteobl	bone
49	chr12:56663200-56680800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:56663200-56685600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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