Variant report

Variant	rs865474
Chromosome Location	chr3:98445324-98445325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs115931	0.96[CEU][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1440158	0.81[JPT][hapmap]
rs278363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278370	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs278373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs278374	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs3755569	0.81[CHD][hapmap]
rs7634817	0.83[MEX][hapmap]
rs828589	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828593	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828594	0.82[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828595	0.96[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs828596	0.82[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs828597	0.82[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs828598	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs828599	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828602	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs828613	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs844159	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844161	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs893831	0.82[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs893832	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9879927	0.80[CHD][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1003922	chr3:98410967-98453602	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv536662	chr3:98410967-98453602	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs865474	ST3GAL6-AS1	cis	Heart Left Ventricle	GTEx
rs865474	OR5K1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98431000-98449200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:98433400-98446000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:98443000-98446200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:98443800-98450800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:98444000-98450800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:98444400-98446800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:98444600-98445400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:98444600-98445400	Enhancers	Osteobl	bone
9	chr3:98444800-98445400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:98444800-98445400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:98444800-98449400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:98445000-98445400	Enhancers	HUVEC	blood vessel
13	chr3:98445000-98446400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:98445200-98446200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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