Variant report

Variant	rs1660690
Chromosome Location	chr6:147490398-147490399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:147486603..147490709-chr6:147522349..147526252,7	K562	blood:
2	chr6:147487150..147489403-chr6:147490355..147493952,4	K562	blood:
3	chr6:147477631..147490692-chr6:147521132..147530003,24	K562	blood:
4	chr6:147487237..147491154-chr6:147494860..147497509,4	K562	blood:
5	chr6:147482480..147485033-chr6:147490242..147491745,2	MCF-7	breast:
6	chr6:147489304..147492300-chr6:147501253..147503085,2	K562	blood:

Variant related genes	Relation type
ENSG00000233452	Chromatin interaction
ENSG00000164506	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1031012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031013	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1221645	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2818866	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818868	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs559038	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594981	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs631931	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652831	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693573	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694625	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.84[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	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886751	chr6:147354092-147490398	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147483000-147491000	Weak transcription	NH-A	brain
2	chr6:147486000-147491200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:147486800-147492600	Enhancers	NHDF-Ad	bronchial
4	chr6:147487200-147493000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:147488000-147490800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:147488200-147490800	Weak transcription	NHEK	skin
7	chr6:147488600-147490600	Weak transcription	HSMM	muscle
8	chr6:147488800-147490800	Weak transcription	HMEC	breast
9	chr6:147488800-147491800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:147488800-147495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:147489000-147490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:147489000-147491800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:147489000-147492600	Weak transcription	K562	blood
14	chr6:147489000-147494200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:147489200-147491000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:147489400-147490800	Weak transcription	NHLF	lung
17	chr6:147489400-147493000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:147489600-147494600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:147489800-147490800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:147490000-147490400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:147490000-147490400	Weak transcription	Osteobl	bone

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