Variant report

Variant	rs6539104
Chromosome Location	chr12:104253431-104253432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104221407..104223311-chr12:104252551..104254594,2	MCF-7	breast:
2	chr12:104252726..104255857-chr12:104256920..104259686,3	MCF-7	breast:
3	chr12:104252720..104255183-chr12:104502836..104504925,2	K562	blood:
4	chr12:104234105..104239098-chr12:104250004..104255076,13	MCF-7	breast:
5	chr12:104247921..104249635-chr12:104251344..104253746,2	MCF-7	breast:
6	chr12:104164135..104167659-chr12:104253252..104255970,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10745986	0.84[EUR][1000 genomes]
rs10745987	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10745988	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10745990	0.84[EUR][1000 genomes]
rs10778297	0.84[EUR][1000 genomes]
rs10778298	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10778299	0.84[EUR][1000 genomes]
rs10778300	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10778302	0.84[EUR][1000 genomes]
rs10778303	0.83[EUR][1000 genomes]
rs10778304	0.83[EUR][1000 genomes]
rs10861124	0.87[JPT][hapmap]
rs10861126	0.86[EUR][1000 genomes]
rs10861134	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10861135	0.84[EUR][1000 genomes]
rs10861136	0.83[EUR][1000 genomes]
rs10861137	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10861139	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10861140	0.83[EUR][1000 genomes]
rs11111816	0.98[ASN][1000 genomes]
rs11111817	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11111823	0.84[EUR][1000 genomes]
rs11111824	0.84[EUR][1000 genomes]
rs11111858	0.87[JPT][hapmap]
rs11613427	0.84[EUR][1000 genomes]
rs1165666	0.88[JPT][hapmap]
rs1165677	0.88[JPT][hapmap]
rs1165678	0.88[JPT][hapmap]
rs1165682	0.88[JPT][hapmap]
rs1183212	0.88[JPT][hapmap]
rs12368121	0.82[JPT][hapmap]
rs12368164	0.81[JPT][hapmap]
rs1866070	0.87[JPT][hapmap]
rs2251979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2252000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2252088	0.98[ASN][1000 genomes]
rs2263954	0.98[ASN][1000 genomes]
rs2374350	0.84[EUR][1000 genomes]
rs2374351	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2374352	0.84[EUR][1000 genomes]
rs2438116	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs2438389	0.98[ASN][1000 genomes]
rs2888809	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2888810	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs3850016	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs3850017	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs3850018	0.84[EUR][1000 genomes]
rs3850019	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs3850020	0.83[EUR][1000 genomes]
rs4491322	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4511355	0.84[EUR][1000 genomes]
rs4964118	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4964308	0.84[EUR][1000 genomes]
rs4964322	0.84[EUR][1000 genomes]
rs4964323	0.84[EUR][1000 genomes]
rs4964326	0.83[EUR][1000 genomes]
rs4964327	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4964328	0.83[EUR][1000 genomes]
rs4964329	0.83[EUR][1000 genomes]
rs4964330	0.83[EUR][1000 genomes]
rs6539109	0.83[EUR][1000 genomes]
rs6539110	0.84[EUR][1000 genomes]
rs7136272	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7136297	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7138145	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7138345	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7138361	0.84[EUR][1000 genomes]
rs7294443	0.84[EUR][1000 genomes]
rs7295172	0.83[EUR][1000 genomes]
rs7295268	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7295285	0.83[EUR][1000 genomes]
rs7295499	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7298496	0.84[EUR][1000 genomes]
rs7298653	0.84[EUR][1000 genomes]
rs7298655	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7299349	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7301119	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7301439	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7302074	0.88[JPT][hapmap]
rs7310988	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7311473	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7314790	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7488952	0.84[EUR][1000 genomes]
rs7956005	0.83[EUR][1000 genomes]
rs7956297	0.83[EUR][1000 genomes]
rs7957036	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957862	0.81[EUR][1000 genomes]
rs7964542	0.84[EUR][1000 genomes]
rs7964654	0.89[CEU][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7971070	0.84[EUR][1000 genomes]
rs7971105	0.84[EUR][1000 genomes]
rs7979423	0.83[EUR][1000 genomes]
rs7979748	0.82[EUR][1000 genomes]
rs9888379	0.83[EUR][1000 genomes]
rs9943761	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9943762	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9943812	0.81[EUR][1000 genomes]
rs9943844	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9988931	0.89[CEU][hapmap];0.84[EUR][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	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
2	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
rs6539104	GNN	cis	parietal	SCAN
rs6539104	TU12B1-TY	cis	multi-tissue	Pritchard
rs6539104	NR1H4	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104253600	Weak transcription	Gastric	stomach
2	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:104246800-104254000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:104250000-104257000	Weak transcription	Pancreas	Pancrea
5	chr12:104250000-104263800	Weak transcription	Liver	Liver
6	chr12:104250400-104254000	Weak transcription	Ovary	ovary
7	chr12:104251200-104254400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:104251400-104254400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:104252000-104254000	Enhancers	HSMMtube	muscle
10	chr12:104252000-104254400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:104252200-104254400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:104252200-104254400	Enhancers	HSMM	muscle
13	chr12:104252200-104254600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:104252200-104254800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:104252200-104254800	Enhancers	Stomach Smooth Muscle	stomach
16	chr12:104252200-104255000	Enhancers	HMEC	breast
17	chr12:104252200-104255800	Enhancers	Placenta	Placenta
18	chr12:104252400-104253800	Enhancers	Fetal Intestine Large	intestine
19	chr12:104252400-104254000	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr12:104252400-104254000	Enhancers	NH-A	brain
21	chr12:104252400-104254200	Enhancers	NHLF	lung
22	chr12:104252400-104254400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:104252400-104254400	Enhancers	NHDF-Ad	bronchial
24	chr12:104252400-104255000	Enhancers	Colon Smooth Muscle	Colon
25	chr12:104252600-104253600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:104252600-104253800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:104252600-104253800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:104252600-104253800	Enhancers	Fetal Intestine Small	intestine
29	chr12:104252600-104253800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:104252600-104253800	Enhancers	HUVEC	blood vessel
31	chr12:104252600-104253800	Enhancers	K562	blood
32	chr12:104252600-104254000	Enhancers	Osteobl	bone
33	chr12:104252600-104254400	Enhancers	Esophagus	oesophagus
34	chr12:104252600-104254400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr12:104252600-104254800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:104252600-104255000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:104252800-104253600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:104252800-104253800	Enhancers	Stomach Mucosa	stomach
39	chr12:104252800-104254400	Enhancers	Fetal Stomach	stomach
40	chr12:104253000-104254400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:104253200-104253600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:104253200-104253600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:104253200-104253600	Flanking Active TSS	A549	lung
44	chr12:104253200-104254200	Flanking Active TSS	Hela-S3	cervix
45	chr12:104253200-104254800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr12:104253400-104253600	Bivalent Enhancer	HepG2	liver
47	chr12:104253400-104253800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:104253400-104254200	Enhancers	Aorta	Aorta
49	chr12:104253400-104254400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links