Variant report

Variant	rs8178610
Chromosome Location	chr3:93646396-93646397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12492553	0.84[EUR][1000 genomes]
rs12634349	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs13085785	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs2965	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap]
rs34309901	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs34411239	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34557251	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35793773	0.84[EUR][1000 genomes]
rs35815512	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs4857146	0.85[EUR][1000 genomes]
rs6123	0.83[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs6764203	0.85[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6765621	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs6777479	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs6791811	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs7428007	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7633544	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs7644769	0.92[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs7653521	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs8178603	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8178613	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8178616	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8178623	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8178630	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921727	0.84[CEU][hapmap]
rs9844676	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834764	chr3:93518281-93677166	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a
2	nsv1002292	chr3:93519466-93736214	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
3	nsv998051	chr3:93519466-93740680	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
4	nsv1005328	chr3:93519466-93743921	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
5	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
7	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv533358	chr3:93575289-93745823	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
12	nsv916541	chr3:93575289-93758589	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
13	esv1803747	chr3:93602038-93759079	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
14	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
15	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
16	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8178610	STX19	cis	parietal	SCAN
rs8178610	NSUN3	cis	Liver	GTEx
rs8178610	HSS00009153	cis	multi-tissue	Pritchard
rs8178610	OR5K2	cis	cerebellum	SCAN
rs8178610	DHFRL1	cis	cerebellum	SCAN
rs8178610	ARL6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93611200-93650400	Weak transcription	Left Ventricle	heart
2	chr3:93626400-93647600	Weak transcription	Ovary	ovary
3	chr3:93633200-93650800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:93633200-93653200	Weak transcription	HepG2	liver
5	chr3:93635200-93653600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:93637000-93650600	Weak transcription	Aorta	Aorta
7	chr3:93642200-93653800	Weak transcription	K562	blood
8	chr3:93642600-93651600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:93644400-93646400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:93644600-93649000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:93645800-93646600	Enhancers	Liver	Liver

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