Variant report

Variant	rs17094560
Chromosome Location	chr12:44769768-44769769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10506243	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10506244	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10506245	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11182470	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11182477	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12300292	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1527315	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17094382	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094386	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094396	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094401	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17094405	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17094408	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17094412	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17094421	0.92[EUR][1000 genomes]
rs17094423	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17094437	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17094458	0.92[EUR][1000 genomes]
rs17094465	1.00[EUR][1000 genomes]
rs17094473	1.00[EUR][1000 genomes]
rs17094505	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17094509	1.00[EUR][1000 genomes]
rs17094532	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17094577	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1716605	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1726889	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1948424	0.92[EUR][1000 genomes]
rs2080876	0.92[EUR][1000 genomes]
rs3858725	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4307772	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4544066	0.85[EUR][1000 genomes]
rs4573751	0.92[EUR][1000 genomes]
rs73276261	0.92[EUR][1000 genomes]
rs74084494	0.92[EUR][1000 genomes]
rs7953537	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7953992	0.92[EUR][1000 genomes]
rs7966220	0.92[EUR][1000 genomes]
rs7975491	0.85[EUR][1000 genomes]
rs840774	1.00[CEU][hapmap];1.00[EUR][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	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
2	nsv1038498	chr12:44679455-44816572	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv826356	chr12:44725069-44783443	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17094560	MDK	trans	brain	seeQTL
rs17094560	HSPA6	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44699000-44782000	Weak transcription	Aorta	Aorta
2	chr12:44754000-44775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:44760200-44770400	Weak transcription	Left Ventricle	heart
4	chr12:44762000-44777400	Weak transcription	Fetal Intestine Small	intestine
5	chr12:44762000-44791200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:44764600-44770600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:44766600-44771400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:44767200-44770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:44767400-44773000	Weak transcription	HMEC	breast
10	chr12:44768200-44773400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:44769000-44772400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:44769600-44769800	Enhancers	Psoas Muscle	Psoas
13	chr12:44769600-44769800	Flanking Active TSS	GM12878-XiMat	blood
14	chr12:44769600-44770000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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