Variant report

Variant	rs12207643
Chromosome Location	chr6:39250778-39250779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39196048..39198749-chr6:39250346..39251924,2	MCF-7	breast:
2	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
3	chr6:39196660..39199150-chr6:39250070..39252621,3	K562	blood:
4	chr6:39246522..39249278-chr6:39249658..39251560,2	MCF-7	breast:
5	chr6:39196660..39199150-chr6:39250070..39252621,2	K562	blood:
6	chr6:39249494..39252314-chr6:39258691..39261153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005951	0.82[ASN][1000 genomes]
rs1005952	0.82[ASN][1000 genomes]
rs10947801	0.97[ASN][1000 genomes]
rs10947802	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11753890	0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11961984	0.87[ASN][1000 genomes]
rs12194671	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12195376	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12202277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12202455	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12209091	0.97[ASN][1000 genomes]
rs12210847	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12211098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214600	0.92[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13194563	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13214473	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535497	0.90[ASN][1000 genomes]
rs1885616	0.97[ASN][1000 genomes]
rs1885617	0.97[ASN][1000 genomes]
rs1885618	0.97[ASN][1000 genomes]
rs1885621	0.97[ASN][1000 genomes]
rs2208791	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2758861	0.80[ASN][1000 genomes]
rs2758882	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758883	0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758884	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758885	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758887	0.97[ASN][1000 genomes]
rs2758888	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758889	0.97[ASN][1000 genomes]
rs2758890	0.97[ASN][1000 genomes]
rs2758891	0.97[ASN][1000 genomes]
rs2758893	0.97[ASN][1000 genomes]
rs2758894	0.97[ASN][1000 genomes]
rs2758895	0.94[ASN][1000 genomes]
rs2758897	0.97[ASN][1000 genomes]
rs2758898	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758899	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2758900	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2815016	0.85[ASN][1000 genomes]
rs2815048	0.97[ASN][1000 genomes]
rs2815049	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815050	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815051	0.97[ASN][1000 genomes]
rs2815052	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815053	0.90[ASN][1000 genomes]
rs2815054	0.97[ASN][1000 genomes]
rs2815057	0.97[ASN][1000 genomes]
rs36044810	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714234	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714235	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59582961	0.95[ASN][1000 genomes]
rs62397165	0.85[ASN][1000 genomes]
rs62397166	0.90[ASN][1000 genomes]
rs62397167	0.97[ASN][1000 genomes]
rs62397168	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71556989	0.95[ASN][1000 genomes]
rs734408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369113	1.00[YRI][hapmap]
rs9380850	1.00[YRI][hapmap]
rs9394588	1.00[YRI][hapmap]
rs9462515	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471043	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9471045	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12207643	LOC221442	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39246200-39251000	Enhancers	Liver	Liver
2	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
4	chr6:39248800-39252800	Weak transcription	Spleen	Spleen
5	chr6:39249400-39250800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:39249600-39253200	Weak transcription	Gastric	stomach
7	chr6:39249800-39251800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:39250000-39251800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr6:39250600-39252800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links