Variant report

Variant	rs4309196
Chromosome Location	chr12:72740262-72740263
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11612036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12302831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12309288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12321111	1.00[CHB][hapmap]
rs12321257	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs12321315	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs12321379	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap]
rs12322759	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17111049	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4390383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4533084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4760760	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs7488259	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs7962187	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7970459	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7970646	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4309196	RAB3IP	cis	cerebellum	SCAN
rs4309196	TBC1D15	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72737200-72740600	Weak transcription	Psoas Muscle	Psoas
2	chr12:72739400-72740600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:72739400-72740800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:72739400-72741000	Enhancers	Brain Cingulate Gyrus	brain
5	chr12:72739400-72741000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr12:72739400-72741200	Enhancers	Brain Angular Gyrus	brain
7	chr12:72739400-72741200	Enhancers	Brain Hippocampus Middle	brain
8	chr12:72739400-72741200	Enhancers	Brain Substantia Nigra	brain
9	chr12:72739400-72741600	Enhancers	Brain Anterior Caudate	brain
10	chr12:72739800-72740800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:72740000-72740600	Enhancers	Skeletal Muscle Female	skeletal muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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