Variant report

Variant	rs578032
Chromosome Location	chr3:54687361-54687362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11707823	0.81[ASN][1000 genomes]
rs1346407	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs2360021	0.95[CHB][hapmap]
rs2360026	0.91[CHB][hapmap]
rs3732748	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4384925	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs496625	0.84[CHD][hapmap]
rs515920	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs517729	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs517738	0.92[ASN][1000 genomes]
rs521694	0.84[ASN][1000 genomes]
rs527297	0.91[ASN][1000 genomes]
rs550210	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs583190	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs587384	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs589281	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs604132	0.83[ASN][1000 genomes]
rs646929	0.85[GIH][hapmap]
rs652424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6809466	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs838022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934083	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs578032	FAM116A	cis	parietal	SCAN
rs578032	SRRD	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54677400-54690800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:54677800-54687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:54681200-54694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:54681400-54693400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:54681600-54693400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:54681800-54693200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:54683600-54693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:54684200-54694600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:54685200-54704000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:54685400-54689200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:54685600-54687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:54686200-54687400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:54686200-54687400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:54686200-54689200	Enhancers	HMEC	breast
15	chr3:54686200-54694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:54686400-54687600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:54686400-54688800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:54686400-54689000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:54686800-54687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:54687000-54688800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:54687200-54688000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:54687200-54688000	Enhancers	GM12878-XiMat	blood
23	chr3:54687200-54688800	Weak transcription	Esophagus	oesophagus
24	chr3:54687200-54688800	Enhancers	NHEK	skin

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