Variant report

Variant	rs2142980
Chromosome Location	chr6:146080679-146080680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146055254..146057948-chr6:146078692..146080698,2	K562	blood:
2	chr6:146054115..146058275-chr6:146075564..146080961,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270638	Chromatin interaction
ENSG00000112425	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1011597	0.95[JPT][hapmap]
rs1062068	0.85[JPT][hapmap]
rs1070518	0.84[ASN][1000 genomes]
rs10872580	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs11155438	0.95[JPT][hapmap]
rs12199362	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1292333	0.95[JPT][hapmap]
rs1292334	0.95[JPT][hapmap]
rs1337841	0.95[JPT][hapmap]
rs1415744	0.95[JPT][hapmap]
rs1415746	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1415747	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1890170	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890171	0.95[JPT][hapmap]
rs1970306	0.99[ASN][1000 genomes]
rs2050027	0.95[JPT][hapmap]
rs2064185	0.95[JPT][hapmap]
rs2142978	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2206142	0.88[ASN][1000 genomes]
rs2223411	0.92[ASN][1000 genomes]
rs2235481	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2246132	0.96[ASN][1000 genomes]
rs2247666	0.85[JPT][hapmap]
rs2249386	0.85[JPT][hapmap]
rs2253654	0.85[JPT][hapmap]
rs2253757	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2265475	0.96[ASN][1000 genomes]
rs2328709	0.80[ASN][1000 genomes]
rs2485631	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34541797	0.91[ASN][1000 genomes]
rs3811102	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3924499	0.85[JPT][hapmap]
rs3924502	0.86[JPT][hapmap]
rs4075694	0.86[JPT][hapmap]
rs4398765	0.83[ASN][1000 genomes]
rs4895683	0.95[JPT][hapmap]
rs4896832	0.95[JPT][hapmap]
rs4896837	0.95[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4896844	0.81[ASN][1000 genomes]
rs62435775	1.00[ASN][1000 genomes]
rs6570701	0.95[JPT][hapmap]
rs6570708	0.95[JPT][hapmap]
rs6570713	0.81[ASN][1000 genomes]
rs6570732	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6900175	0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6901888	0.95[JPT][hapmap]
rs6906258	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6906402	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6915718	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6922507	0.86[JPT][hapmap]
rs6923545	0.85[JPT][hapmap]
rs6930154	0.95[JPT][hapmap]
rs6931553	0.80[ASN][1000 genomes]
rs6941429	0.95[JPT][hapmap]
rs697053	0.95[JPT][hapmap]
rs697054	0.95[JPT][hapmap]
rs697055	0.95[JPT][hapmap]
rs702304	0.95[JPT][hapmap]
rs702306	0.95[JPT][hapmap]
rs702307	0.95[JPT][hapmap]
rs702316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs702322	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7752286	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7753092	0.86[JPT][hapmap]
rs7753273	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7753696	0.86[JPT][hapmap]
rs7753770	0.95[JPT][hapmap]
rs857875	0.95[JPT][hapmap]
rs857877	0.95[JPT][hapmap]
rs857880	0.95[JPT][hapmap]
rs857881	0.95[JPT][hapmap]
rs857882	0.95[JPT][hapmap]
rs857883	0.95[JPT][hapmap]
rs9285508	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9373467	0.89[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs9373475	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9376961	0.95[JPT][hapmap]
rs9376965	1.00[ASN][1000 genomes]
rs9376970	0.85[JPT][hapmap]
rs9386132	0.80[ASN][1000 genomes]
rs9386134	0.80[ASN][1000 genomes]
rs9386136	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9390356	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9390365	0.86[JPT][hapmap]
rs9399561	0.95[JPT][hapmap]
rs9403737	0.95[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9403742	0.85[JPT][hapmap]
rs9403749	0.85[JPT][hapmap]
rs9403756	0.85[JPT][hapmap]
rs9485017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9497395	0.81[JPT][hapmap]
rs9497403	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9497426	0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs9497431	0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146079000-146081000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr6:146080000-146081000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:146080000-146084200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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