Variant report

Variant	rs3953686
Chromosome Location	chr9:99924604-99924605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10739337	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10759496	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759542	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10759547	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10759605	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10759610	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10759619	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs10817300	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10817306	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs10817361	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs10817403	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs10817448	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10981528	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10981551	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10981560	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs10981625	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs12683119	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12683933	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1462086	0.87[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs1462087	0.88[CEU][hapmap]
rs1462092	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1841683	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1857084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1870859	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1935372	0.83[AFR][1000 genomes]
rs2003205	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2061634	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs2061635	0.87[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2255135	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2255139	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2401382	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2447290	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2487874	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs2493444	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2502646	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2615144	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2795363	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2795366	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap]
rs2795369	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2795370	0.96[CEU][hapmap]
rs2818236	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2818240	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2818241	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2818242	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2818244	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2859564	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs2888960	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs3994559	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs4300106	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345679	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs4437755	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs4742683	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4743075	0.88[CEU][hapmap]
rs4743080	0.88[CEU][hapmap]
rs6477982	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6477988	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6477993	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6478008	0.84[AMR][1000 genomes]
rs6478043	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6478048	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6478059	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7020002	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7021895	0.84[AMR][1000 genomes]
rs7023087	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7026287	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7026893	0.87[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7029749	0.88[CEU][hapmap]
rs7047367	0.83[AFR][1000 genomes]
rs725228	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs752243	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7847332	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs7855385	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7855956	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs7863530	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7867330	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7875158	0.83[AFR][1000 genomes]
rs9299202	0.96[CEU][hapmap];0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs9409139	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS 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	9 gene(s)	inside rSNPs	diseases
2	nsv972432	chr9:99874607-99958095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv969695	chr9:99924101-99925101	Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3953686	RP11-23J9.4	cis	Artery Tibial	GTEx
rs3953686	CCDC180	cis	Artery Tibial	GTEx
rs3953686	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99911600-99957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:99913400-99930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:99913600-99930800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99922800-99926200	Weak transcription	Dnd41	blood
8	chr9:99923600-99932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:99923800-99927000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:99923800-99936200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:99924200-99925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:99924200-99926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:99924400-99926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:99924600-99926000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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