Variant report

Variant	rs617956
Chromosome Location	chr12:10146236-10146237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10772223	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10772224	0.81[AMR][1000 genomes]
rs1447888	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs1746123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2273986	0.96[ASN][1000 genomes]
rs2760953	0.81[CHB][hapmap]
rs4764178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4764179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4764180	0.88[ASN][1000 genomes]
rs4764181	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs476564	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs477658	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs525013	0.81[CHB][hapmap]
rs526157	0.81[CHB][hapmap]
rs542700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs566505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs581949	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs582968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs584856	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs613871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640817	0.81[CHB][hapmap]
rs6488241	0.81[AMR][1000 genomes]
rs7977955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7977964	0.96[ASN][1000 genomes]
rs7980924	0.96[ASN][1000 genomes]
rs935538	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898755	chr12:10069302-10186284	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043125	chr12:10121288-10177037	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1042106	chr12:10121288-10177636	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1040610	chr12:10121288-10179374	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525593	chr12:10121347-10156646	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv898756	chr12:10142538-10174314	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv604	chr12:10144039-10160440	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs617956	CLEC12A	cis	Nerve Tibial	GTEx
rs617956	RP11-133L14.5	cis	Nerve Tibial	GTEx
rs617956	CLEC12B	cis	Whole Blood	GTEx
rs617956	CLEC12B	cis	Nerve Tibial	GTEx
rs617956	CLEC12A	cis	Adipose Subcutaneous	GTEx
rs617956	CLEC12A	cis	Artery Tibial	GTEx
rs617956	RP11-133L14.5	cis	Whole Blood	GTEx
rs617956	CLEC12A	cis	Muscle Skeletal	GTEx
rs617956	CLEC1B	cis	Nerve Tibial	GTEx
rs617956	CLEC12A	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10145200-10155400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr12:10145200-10155800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10145800-10153400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:10146000-10146400	Enhancers	Brain Angular Gyrus	brain
5	chr12:10146000-10146400	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links