Variant report

Variant	rs7307916
Chromosome Location	chr12:31796157-31796158
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10771860	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10843977	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10843980	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10843981	0.86[AMR][1000 genomes]
rs10843982	0.85[AMR][1000 genomes]
rs10843983	0.89[AMR][1000 genomes]
rs10843984	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843985	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843986	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051501	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11051505	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051506	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11051507	0.91[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051508	0.91[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051509	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051511	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11608917	0.84[AMR][1000 genomes]
rs11608932	0.84[AMR][1000 genomes]
rs11611053	0.81[AMR][1000 genomes]
rs12366487	0.85[AMR][1000 genomes]
rs12368226	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12813290	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2046367	0.86[ASN][1000 genomes]
rs2046368	0.81[AMR][1000 genomes]
rs2374165	0.91[CEU][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs2374167	0.88[AMR][1000 genomes]
rs2374168	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2888753	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2888754	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34312039	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34399504	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3844104	0.84[AMR][1000 genomes]
rs3908176	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4346052	0.81[ASN][1000 genomes]
rs4931530	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4931531	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4931532	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931533	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4999141	0.88[AMR][1000 genomes]
rs55935178	0.84[AMR][1000 genomes]
rs56320129	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57741885	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61930405	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6487997	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6487998	0.91[CEU][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6487999	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7299690	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7313475	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7313596	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7314164	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7962168	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7967222	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7307916	PTHLH	cis	cerebellum	SCAN
rs7307916	DENND5B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31783400-31803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:31783400-31803000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:31789600-31803000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:31789800-31801200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:31789800-31803000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:31794800-31799800	Weak transcription	Fetal Kidney	kidney
7	chr12:31795400-31798000	Weak transcription	HepG2	liver
8	chr12:31796000-31797200	Weak transcription	Ovary	ovary
9	chr12:31796000-31797200	Weak transcription	Pancreas	Pancrea

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