Variant report

Variant	rs12176359
Chromosome Location	chr6:36665012-36665013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36644113..36646429-chr6:36664735..36667230,2	K562	blood:
2	chr6:36662298..36665035-chr6:36665168..36667578,2	MCF-7	breast:
3	chr6:36664831..36667181-chr6:36668098..36669647,2	MCF-7	breast:
4	chr6:36658383..36660114-chr6:36663933..36665549,2	MCF-7	breast:
5	chr6:36650057..36652668-chr6:36663338..36666266,2	K562	blood:
6	chr6:36650715..36656032-chr6:36664945..36667924,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11750955	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[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753407	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972291	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35442158	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72853397	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756867	0.91[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs9349006	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349007	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9368955	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9380589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380590	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380591	0.81[EUR][1000 genomes]
rs9380592	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394376	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885808	chr6:36659932-36684518	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3343209	chr6:36663774-36668072	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12176359	GRM4	cis	cerebellum	SCAN
rs12176359	FLJ43093	cis	multi-tissue	Pritchard
rs12176359	SRSF3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36655000-36672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:36655200-36669400	Weak transcription	Gastric	stomach
3	chr6:36656200-36665200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36659800-36665800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:36660600-36666400	Enhancers	Primary B cells from cord blood	blood
6	chr6:36660800-36665200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:36660800-36665200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:36660800-36665200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:36660800-36666800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:36661000-36665200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:36661000-36667000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:36661200-36666000	Weak transcription	Stomach Mucosa	stomach
13	chr6:36661200-36668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:36661400-36665200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:36661400-36665200	Weak transcription	Esophagus	oesophagus
16	chr6:36661400-36665200	Weak transcription	Spleen	Spleen
17	chr6:36661400-36696400	Weak transcription	Right Atrium	heart
18	chr6:36663200-36666400	Weak transcription	Fetal Heart	heart
19	chr6:36664000-36665200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr6:36664000-36665600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:36664600-36665200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:36664600-36665600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:36664800-36668600	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links