Variant report

Variant	rs7953173
Chromosome Location	chr12:44488756-44488757
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	chr12:43184139..43186103-chr12:44487352..44490285,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10506234	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506238	0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11613902	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs11830719	0.85[CHB][hapmap]
rs11837611	0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12099550	0.86[EUR][1000 genomes]
rs12297529	1.00[TSI][hapmap]
rs12315961	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs1352935	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[ASN][1000 genomes]
rs17094063	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs17094097	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17094102	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17094110	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17094117	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs17094119	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28495612	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28838075	0.90[ASN][1000 genomes]
rs55950371	0.93[ASN][1000 genomes]
rs58851540	0.86[EUR][1000 genomes]
rs59628873	0.90[ASN][1000 genomes]
rs60026566	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61399923	0.93[ASN][1000 genomes]
rs6582498	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs68049983	0.90[ASN][1000 genomes]
rs7137787	0.85[CHB][hapmap]
rs7298069	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7298835	1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73272204	0.82[AFR][1000 genomes]
rs73272217	0.81[AFR][1000 genomes]
rs73286295	0.86[EUR][1000 genomes]
rs73286296	0.86[EUR][1000 genomes]
rs73286301	0.86[EUR][1000 genomes]
rs73288025	0.86[EUR][1000 genomes]
rs73288036	0.86[EUR][1000 genomes]
rs73288050	0.90[ASN][1000 genomes]
rs73288052	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73288054	0.86[EUR][1000 genomes]
rs73288073	0.86[EUR][1000 genomes]
rs73288075	0.86[EUR][1000 genomes]
rs73288080	0.86[EUR][1000 genomes]
rs73288085	0.86[EUR][1000 genomes]
rs73288089	0.86[EUR][1000 genomes]
rs73288095	0.86[EUR][1000 genomes]
rs73290203	0.86[EUR][1000 genomes]
rs73290206	0.86[EUR][1000 genomes]
rs73290208	0.86[EUR][1000 genomes]
rs73290213	0.86[EUR][1000 genomes]
rs73290217	0.86[EUR][1000 genomes]
rs73290223	0.86[EUR][1000 genomes]
rs73290224	0.86[EUR][1000 genomes]
rs73290228	0.86[EUR][1000 genomes]
rs73290230	0.86[EUR][1000 genomes]
rs7961986	0.81[AFR][1000 genomes]
rs7967819	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7967957	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs7968777	0.85[CHB][hapmap]
rs7971340	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7980383	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs842207	0.86[CHB][hapmap]
rs860867	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs9738149	0.85[CHB][hapmap]

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	nsv832390	chr12:44318071-44512114	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1041188	chr12:44331098-44528712	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832391	chr12:44394137-44552555	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7953173	MTTP	trans	brain	seeQTL
rs7953173	NUP210	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44469400-44495600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:44482800-44501000	Weak transcription	Left Ventricle	heart
3	chr12:44484600-44488800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:44486400-44491800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links