Variant report

Variant	rs9348777
Chromosome Location	chr6:27743878-27743879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27738868..27742221-chr6:27743370..27745719,4	MCF-7	breast:
2	chr6:27483274..27486299-chr6:27743798..27746075,3	K562	blood:
3	chr6:27114542..27117845-chr6:27741589..27745932,6	K562	blood:
4	chr6:27100048..27102591-chr6:27743747..27745721,2	K562	blood:
5	chr6:27100313..27102591-chr6:27743747..27746593,3	K562	blood:
6	chr6:27113969..27118292-chr6:27739764..27746039,7	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10484400	0.91[EUR][1000 genomes]
rs10946943	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs1157432	0.88[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12055685	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs12173985	0.91[EUR][1000 genomes]
rs12174087	0.90[EUR][1000 genomes]
rs12663707	0.91[EUR][1000 genomes]
rs12664599	0.91[EUR][1000 genomes]
rs1555021	0.91[EUR][1000 genomes]
rs1565334	0.86[CHB][hapmap]
rs16867886	0.91[EUR][1000 genomes]
rs16867916	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs16867921	0.90[EUR][1000 genomes]
rs16867976	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16868156	0.86[CHB][hapmap]
rs1973889	0.91[EUR][1000 genomes]
rs3175123	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34452669	0.85[ASN][1000 genomes]
rs3800321	0.86[CHB][hapmap]
rs56408767	0.91[EUR][1000 genomes]
rs59893892	0.90[EUR][1000 genomes]
rs60096640	0.81[EUR][1000 genomes]
rs6906653	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs6920044	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs73385147	0.91[EUR][1000 genomes]
rs73385152	0.91[EUR][1000 genomes]
rs73385154	0.91[EUR][1000 genomes]
rs7753236	0.90[EUR][1000 genomes]
rs878241	0.91[EUR][1000 genomes]
rs9295751	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs9348771	0.91[EUR][1000 genomes]
rs9348778	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357043	0.91[EUR][1000 genomes]
rs9357044	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs9357048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368517	0.90[EUR][1000 genomes]
rs9368521	0.91[EUR][1000 genomes]
rs9368524	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs9368525	0.88[EUR][1000 genomes]
rs9368526	0.91[EUR][1000 genomes]
rs9368538	0.86[CHB][hapmap]
rs9380000	0.90[EUR][1000 genomes]
rs9380001	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs9380005	0.88[EUR][1000 genomes]
rs9380022	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs9380024	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9393826	0.87[CHB][hapmap]
rs9393832	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs9393842	0.91[EUR][1000 genomes]
rs9393849	0.90[EUR][1000 genomes]
rs9393852	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393856	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27740200-27745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27740400-27745200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:27741200-27744600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:27741400-27744400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:27741800-27744600	Weak transcription	A549	lung
6	chr6:27741800-27744600	Enhancers	K562	blood
7	chr6:27742200-27744400	Weak transcription	GM12878-XiMat	blood
8	chr6:27742200-27744800	Weak transcription	HepG2	liver
9	chr6:27743000-27744000	Enhancers	Fetal Intestine Large	intestine
10	chr6:27743000-27744000	Enhancers	Fetal Intestine Small	intestine
11	chr6:27743000-27744000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:27743600-27744000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:27743600-27745600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:27743600-27750000	Weak transcription	Rectal Mucosa Donor 29	rectum

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