Variant report

Variant	rs12040141
Chromosome Location	chr1:169501700-169501701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
2	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
3	chr1:169454448..169456119-chr1:169499444..169502094,2	K562	blood:

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap]
rs12022009	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042044	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12733037	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap]
rs13306334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533518	1.00[CEU][hapmap]
rs1533519	1.00[CEU][hapmap]
rs16862097	1.00[CEU][hapmap]
rs16862176	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862180	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862217	1.00[CEU][hapmap]
rs1883167	1.00[CEU][hapmap]
rs2037249	1.00[CEU][hapmap]
rs2271762	1.00[CEU][hapmap]
rs2301517	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap]
rs6008	0.95[EUR][1000 genomes]
rs6020	0.81[CHD][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap]
rs66737090	0.95[EUR][1000 genomes]
rs7551623	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332624	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332647	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332658	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332678	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169494000-169502800	Strong transcription	HepG2	liver
3	chr1:169496000-169515200	Strong transcription	Liver	Liver
4	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
5	chr1:169498600-169506200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:169498600-169507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:169499000-169501800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:169499000-169504200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169499000-169508400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:169499000-169519000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:169499800-169501800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:169500000-169504600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:169500200-169526800	Weak transcription	Left Ventricle	heart
14	chr1:169500800-169503400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:169501600-169504000	Weak transcription	Primary monocytes fromperipheralblood	blood

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