Variant report

Variant	rs6582294
Chromosome Location	chr12:76034992-76034993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76032457..76035300-chr12:76104195..76106631,2	MCF-7	breast:
2	chr12:76032186..76035156-chr12:76036962..76040307,4	K562	blood:
3	chr12:76033638..76035156-chr12:76038536..76041322,2	K562	blood:
4	chr12:76032058..76036488-chr12:76038031..76041740,5	MCF-7	breast:
5	chr12:76032505..76035383-chr12:76043295..76046760,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10785198	0.83[ASN][1000 genomes]
rs10879929	0.81[ASN][1000 genomes]
rs10879932	0.81[ASN][1000 genomes]
rs10879933	0.81[ASN][1000 genomes]
rs10879934	0.82[ASN][1000 genomes]
rs10879935	0.82[ASN][1000 genomes]
rs10879936	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10879945	0.84[GIH][hapmap]
rs10879949	0.98[ASN][1000 genomes]
rs11180575	0.81[ASN][1000 genomes]
rs11180584	0.82[ASN][1000 genomes]
rs11180598	0.92[ASN][1000 genomes]
rs11180603	0.90[ASN][1000 genomes]
rs11519910	0.83[ASN][1000 genomes]
rs11520226	0.83[ASN][1000 genomes]
rs12811250	0.82[ASN][1000 genomes]
rs17115238	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2054516	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366988	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2366989	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs2886828	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34406885	0.81[ASN][1000 genomes]
rs3847671	0.81[ASN][1000 genomes]
rs4882631	0.86[CHB][hapmap]
rs4882635	0.83[ASN][1000 genomes]
rs58886425	0.90[ASN][1000 genomes]
rs60465677	0.84[ASN][1000 genomes]
rs6582293	0.94[ASN][1000 genomes]
rs7137610	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7297580	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305673	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7314159	0.82[ASN][1000 genomes]
rs7314220	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7315474	0.99[ASN][1000 genomes]
rs7956673	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7956953	0.90[ASN][1000 genomes]
rs7958508	0.85[ASN][1000 genomes]
rs7962144	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs7962276	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs7979460	0.90[ASN][1000 genomes]
rs7979600	0.84[ASN][1000 genomes]
rs7980713	0.82[ASN][1000 genomes]
rs9634253	0.91[CHB][hapmap];0.95[JPT][hapmap]

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	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs6582294	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs6582294	GLIPR1L2	cis	Thyroid	GTEx
rs6582294	RP11-585P4.5	cis	Muscle Skeletal	GTEx
rs6582294	GLIPR1L2	cis	Artery Tibial	GTEx
rs6582294	GLIPR1L2	cis	Adipose Subcutaneous	GTEx
rs6582294	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs6582294	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs6582294	GLIPR1L2	cis	cerebellum	SCAN
rs6582294	KRR1	cis	cerebellum	SCAN
rs6582294	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs6582294	RP11-585P4.5	cis	Skin Sun Exposed Lower leg	GTEx
rs6582294	GLIPR1	cis	cerebellum	SCAN
rs6582294	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs6582294	GLIPR1L2	cis	Nerve Tibial	GTEx
rs6582294	GLIPR1L2	cis	lung	GTEx
rs6582294	GLIPR1L2	cis	parietal	SCAN
rs6582294	RP11-585P4.5	cis	Artery Tibial	GTEx
rs6582294	RP11-585P4.5	cis	Nerve Tibial	GTEx
rs6582294	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs6582294	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs6582294	KRR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76026600-76035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:76030400-76035200	Weak transcription	NHLF	lung
3	chr12:76032000-76035800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:76032400-76036800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:76032400-76037200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:76032600-76036800	Enhancers	HMEC	breast
7	chr12:76032800-76036600	Enhancers	NHEK	skin
8	chr12:76033200-76035200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:76033200-76035600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:76033200-76035600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:76033600-76036400	Enhancers	Dnd41	blood
12	chr12:76033800-76035400	Weak transcription	Esophagus	oesophagus
13	chr12:76034000-76036400	Enhancers	A549	lung
14	chr12:76034200-76035600	Enhancers	HepG2	liver
15	chr12:76034200-76036600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:76034200-76036800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:76034400-76035400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr12:76034400-76035400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:76034400-76036400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:76034400-76036800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:76034400-76036800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:76034400-76036800	Enhancers	NHDF-Ad	bronchial
23	chr12:76034600-76035200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:76034600-76035200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:76034600-76035600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:76034600-76035600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:76034600-76035600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:76034600-76035800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:76034600-76035800	Enhancers	K562	blood
30	chr12:76034600-76036600	Enhancers	HSMMtube	muscle
31	chr12:76034600-76036800	Enhancers	HSMM	muscle
32	chr12:76034600-76037200	Enhancers	NH-A	brain
33	chr12:76034800-76035000	Enhancers	GM12878-XiMat	blood
34	chr12:76034800-76035200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:76034800-76035200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr12:76034800-76035200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr12:76034800-76035200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:76034800-76035400	Enhancers	Small Intestine	intestine
39	chr12:76034800-76035600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:76034800-76035600	Enhancers	Primary B cells from peripheral blood	blood
41	chr12:76034800-76035600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:76034800-76035600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr12:76034800-76035600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:76034800-76035600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:76034800-76035600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:76034800-76035600	Flanking Active TSS	Osteobl	bone
47	chr12:76034800-76035800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:76034800-76035800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:76034800-76036600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links