Variant report

Variant	rs496625
Chromosome Location	chr3:54663005-54663006
allele	C/T
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:20)

rs_ID	r²[population]
rs1366032	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs483200	0.92[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs495532	0.82[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs508907	0.88[CEU][hapmap]
rs551799	0.89[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs573279	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs578032	0.84[CHD][hapmap]
rs595040	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs595993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs605284	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs616113	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626074	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs661201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662565	0.82[ASN][1000 genomes]
rs667612	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs670335	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs674542	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838022	0.84[CHD][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
rs496625	RRP9	cis	parietal	SCAN
rs496625	RFT1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54651000-54666400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:54652800-54665000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:54659200-54664600	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:54659800-54664400	Weak transcription	Spleen	Spleen
6	chr3:54660400-54666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:54662400-54663600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr3:54662400-54664600	Enhancers	HMEC	breast
9	chr3:54662400-54665200	Strong transcription	Right Atrium	heart
10	chr3:54662600-54664000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:54662600-54664200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:54662800-54663200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:54662800-54663600	Strong transcription	Ovary	ovary
14	chr3:54662800-54663600	Enhancers	Hela-S3	cervix
15	chr3:54662800-54663800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:54663000-54663200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr3:54663000-54663200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:54663000-54663800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:54663000-54663800	Enhancers	Esophagus	oesophagus
20	chr3:54663000-54664800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:54663000-54666200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:54663000-54667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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