Variant report

Variant	rs3909479
Chromosome Location	chr5:94787954-94787955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94787545..94789529-chr5:94790641..94792240,2	K562	blood:
2	chr5:94779335..94782524-chr5:94785930..94789104,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10463192	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10515227	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949551	0.83[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11960723	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12188620	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17084725	1.00[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17084869	0.88[ASW][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17084916	0.82[ASW][hapmap];0.91[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1964334	0.81[EUR][1000 genomes]
rs55710829	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55839939	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56124625	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57529864	0.93[EUR][1000 genomes]
rs6861524	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6882491	0.90[EUR][1000 genomes]
rs6883612	0.93[EUR][1000 genomes]
rs73141965	0.93[EUR][1000 genomes]
rs73143927	0.93[EUR][1000 genomes]
rs7349776	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7349780	0.81[AFR][1000 genomes]
rs73777195	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73777196	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73777206	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73777207	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73777210	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73777218	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73777223	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73777227	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7534	1.00[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705631	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3909479	TTC37	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94777000-94798600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:94780400-94810800	Weak transcription	Pancreas	Pancrea
3	chr5:94782000-94810200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:94782600-94800000	Weak transcription	HMEC	breast
5	chr5:94783200-94796000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:94783400-94795000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:94783400-94795800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:94783400-94798600	Weak transcription	Gastric	stomach
9	chr5:94783400-94798600	Weak transcription	Left Ventricle	heart
10	chr5:94783600-94797200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:94783600-94798400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:94785000-94798600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:94785000-94798600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:94785200-94796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:94785200-94796000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:94785200-94796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:94785600-94795800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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