Variant report

Variant	rs6936952
Chromosome Location	chr6:27741137-27741138
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27095110..27096779-chr6:27740302..27742676,2	K562	blood:
2	chr6:27739033..27741746-chr6:27859741..27864779,4	MCF-7	breast:
3	chr6:27740321..27742174-chr6:27780434..27782983,2	MCF-7	breast:
4	chr6:27653465..27656102-chr6:27740718..27743462,2	K562	blood:
5	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
6	chr6:27113969..27118292-chr6:27739764..27746039,7	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11962485	1.00[CEU][hapmap]
rs11962868	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11966528	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11966565	1.00[ASN][1000 genomes]
rs11968469	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970638	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs200466	0.87[EUR][1000 genomes]
rs200469	0.87[EUR][1000 genomes]
rs200471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs200473	0.87[EUR][1000 genomes]
rs56002038	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59199903	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60339576	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666846	0.87[EUR][1000 genomes]
rs6901437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906904	1.00[ASN][1000 genomes]
rs6906980	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6915101	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922530	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6933702	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6938018	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384331	1.00[ASN][1000 genomes]
rs73389017	1.00[ASN][1000 genomes]
rs73389037	1.00[ASN][1000 genomes]
rs73389068	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742752	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461422	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9468227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468262	1.00[CEU][hapmap];1.00[CHB][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6936952	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:27738800-27741800	Enhancers	Primary hematopoietic stem cells	blood
5	chr6:27739000-27742000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr6:27739000-27742400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:27739000-27742400	Enhancers	Primary B cells from peripheral blood	blood
8	chr6:27739200-27742200	Enhancers	GM12878-XiMat	blood
9	chr6:27739400-27741600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:27739800-27741200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:27739800-27742400	Enhancers	Primary B cells from cord blood	blood
12	chr6:27740000-27741200	Flanking Active TSS	HepG2	liver
13	chr6:27740000-27741800	Flanking Active TSS	K562	blood
14	chr6:27740000-27742200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:27740000-27742200	Enhancers	Stomach Mucosa	stomach
16	chr6:27740200-27741200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:27740200-27741400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:27740200-27741800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:27740200-27745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:27740400-27741600	Enhancers	Colonic Mucosa	Colon
21	chr6:27740400-27741600	Enhancers	Spleen	Spleen
22	chr6:27740400-27742200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:27740400-27742600	Enhancers	Fetal Intestine Small	intestine
24	chr6:27740400-27745200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:27740600-27741200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:27740600-27741400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:27740600-27741400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:27740800-27741200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
29	chr6:27740800-27741200	Weak transcription	NHEK	skin
30	chr6:27740800-27741800	Enhancers	A549	lung
31	chr6:27740800-27742200	Enhancers	Duodenum Mucosa	Duodenum
32	chr6:27740800-27742600	Enhancers	Fetal Intestine Large	intestine
33	chr6:27740800-27743200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:27741000-27741200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:27741000-27743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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