Variant report

Variant	rs12229038
Chromosome Location	chr12:103746086-103746087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:103745859..103749136-chr12:103750822..103754295,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10507162	1.00[CEU][hapmap]
rs10860976	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10860979	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10860981	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10860982	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11111517	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11111520	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11111522	1.00[CHB][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111525	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111527	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111528	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111529	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111530	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111531	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111532	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111535	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228711	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12230008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343985	1.00[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1343986	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554394	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs17033627	0.92[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs17033705	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2139557	1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs2888728	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144505	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4147493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304883	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764731	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4764950	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4764953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57342939	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57747432	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59259889	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60563650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539067	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7132491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294776	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954263	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7975056	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7980492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv455703	chr12:103692799-103818049	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv560037	chr12:103692799-103818049	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103707200-103786400	Weak transcription	Primary B cells from cord blood	blood
2	chr12:103745000-103746200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr12:103745600-103755800	Weak transcription	Spleen	Spleen
4	chr12:103745800-103750000	Strong transcription	Primary B cells from peripheral blood	blood

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