Variant report

Variant	rs7009406
Chromosome Location	chr8:125067187-125067188
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	chr8:125066380..125069161-chr8:125069847..125072884,3	MCF-7	breast:
2	chr8:125066429..125069307-chr8:125073491..125075703,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM65-5	chr8:125065559-125067194	ucscGeneNc_uc003yqx_1

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10094266	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10094533	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10102566	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10106600	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10113693	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10113772	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1073178	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1075051	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10808530	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10808531	0.99[EUR][1000 genomes]
rs10956163	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes]
rs10956164	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes]
rs11984962	0.85[EUR][1000 genomes]
rs12375254	0.80[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12541155	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12545670	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13251412	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13254252	1.00[CEU][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes]
rs13254498	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13258808	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13258930	0.95[EUR][1000 genomes]
rs13261097	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13263969	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13269044	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2069078	1.00[CEU][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs28550456	0.81[AMR][1000 genomes]
rs3886123	0.80[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs4242353	0.84[EUR][1000 genomes]
rs4294164	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4311644	0.80[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4330676	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4345538	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4389914	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4392878	0.80[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4404895	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4410885	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4412351	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes]
rs4430074	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4446721	0.89[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4460351	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4483140	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4484683	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4510842	0.83[ASW][hapmap];0.91[CEU][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4576412	0.80[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4870886	0.84[EUR][1000 genomes]
rs4871451	0.80[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4871452	0.80[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4871453	0.80[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4871454	0.80[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4871457	0.80[CEU][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4871458	0.80[CEU][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4871459	0.80[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs4871460	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4871461	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4871462	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59583746	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6470214	0.84[EUR][1000 genomes]
rs6470216	1.00[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6470217	0.99[EUR][1000 genomes]
rs6470218	0.98[EUR][1000 genomes]
rs6470219	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6470220	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6470221	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6983060	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs6984093	0.80[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6987082	0.91[CEU][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes]
rs6991629	1.00[CEU][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6995745	0.84[EUR][1000 genomes]
rs7001300	0.80[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs7003992	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7005123	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes]
rs7007739	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7010375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7012186	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7013226	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes]
rs7815620	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs7815768	0.95[EUR][1000 genomes]
rs7816075	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7822018	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7822412	0.88[EUR][1000 genomes]
rs7822557	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7825506	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7826405	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7827412	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7831422	0.80[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7832499	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7836974	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7840702	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7841692	0.84[EUR][1000 genomes]
rs7842213	0.80[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs9297683	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9297684	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9297685	1.00[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs9643188	1.00[CEU][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][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	nsv6375	chr8:125056543-125087258	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv612144	chr8:125057728-125206503	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1023183	chr8:125060532-125206445	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv948556	chr8:125067187-125204721	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125052600-125083600	Weak transcription	Gastric	stomach
2	chr8:125064400-125078600	Weak transcription	Stomach Mucosa	stomach
3	chr8:125065200-125067200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr8:125065400-125067200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:125065800-125067400	Bivalent Enhancer	NHDF-Ad	bronchial
6	chr8:125066200-125067400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:125066200-125071600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:125066400-125068000	Weak transcription	Fetal Stomach	stomach
9	chr8:125066800-125068000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:125066800-125068600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr8:125067000-125067200	Enhancers	Psoas Muscle	Psoas
12	chr8:125067000-125071000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links