Variant report

Variant	rs7296900
Chromosome Location	chr12:104177668-104177669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104166261..104169463-chr12:104174698..104177836,3	MCF-7	breast:
2	chr12:104176398..104178432-chr12:104233589..104235807,2	MCF-7	breast:
3	chr12:104177175..104180567-chr12:104180842..104183516,3	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10735389	0.81[CHD][hapmap]
rs10778285	1.00[ASN][1000 genomes]
rs10861093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10861098	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861099	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861102	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861103	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111761	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111764	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11111766	1.00[ASN][1000 genomes]
rs11111772	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111773	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111775	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111781	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs11111782	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs11111783	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs11111787	0.99[ASN][1000 genomes]
rs12424737	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs12425205	0.84[CHD][hapmap]
rs1370777	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370778	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370779	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1866294	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs1866296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1968513	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888792	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751205	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3812804	0.85[CHD][hapmap]
rs4964813	0.99[ASN][1000 genomes]
rs4964814	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs4964819	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964820	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981034	0.81[CHD][hapmap]
rs4981035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5001722	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61602054	0.97[ASN][1000 genomes]
rs6539101	0.85[CHD][hapmap]
rs7136682	0.91[ASN][1000 genomes]
rs7312606	0.99[ASN][1000 genomes]
rs7312825	0.99[ASN][1000 genomes]
rs73192049	0.96[ASN][1000 genomes]
rs7970553	0.85[CHD][hapmap]
rs7973081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9084	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs934843	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs934846	0.97[ASN][1000 genomes]
rs954921	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs9706225	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7296900	TU12B1-TY	cis	multi-tissue	Pritchard
rs7296900	DEPDC4	cis	cerebellum	SCAN
rs7296900	NT5DC3	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
4	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
5	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:104163000-104178400	Strong transcription	NHEK	skin
7	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
10	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
11	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:104168000-104178800	Weak transcription	Hela-S3	cervix
13	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
14	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:104168600-104180800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:104169200-104180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:104170400-104179200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:104170400-104180400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr12:104170600-104179400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:104171400-104177800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:104171600-104178200	Weak transcription	Primary B cells from cord blood	blood
26	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:104171800-104178200	Weak transcription	Pancreas	Pancrea
29	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
30	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:104172000-104178200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:104173000-104179400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:104173400-104179000	Strong transcription	Ovary	ovary
36	chr12:104173600-104178600	Weak transcription	Fetal Kidney	kidney
37	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:104174000-104178000	Weak transcription	Right Ventricle	heart
39	chr12:104174000-104178200	Weak transcription	Left Ventricle	heart
40	chr12:104174000-104178200	Weak transcription	Lung	lung
41	chr12:104174000-104180400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:104174000-104180400	Strong transcription	HMEC	breast
43	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:104174200-104178200	Weak transcription	GM12878-XiMat	blood
45	chr12:104174200-104179200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:104174200-104179200	Weak transcription	NHDF-Ad	bronchial
47	chr12:104174200-104185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:104174400-104177800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:104174400-104179800	Enhancers	Skeletal Muscle Male	skeletal muscle

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