Variant report

Variant	rs6838613
Chromosome Location	chr4:48476539-48476540
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	chr4:48474711..48478093-chr4:48481760..48484353,3	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10029785	0.95[JPT][hapmap]
rs10938534	0.89[GIH][hapmap]
rs1117010	0.81[ASN][1000 genomes]
rs11737677	0.86[GIH][hapmap]
rs11945562	0.89[GIH][hapmap];0.81[JPT][hapmap]
rs12503644	0.88[ASN][1000 genomes]
rs12507206	0.82[ASN][1000 genomes]
rs12511991	0.82[ASN][1000 genomes]
rs12645501	0.82[CHB][hapmap]
rs12645951	0.95[JPT][hapmap]
rs12649527	0.80[ASN][1000 genomes]
rs12649528	0.80[ASN][1000 genomes]
rs13105385	0.81[ASN][1000 genomes]
rs13115295	0.82[ASN][1000 genomes]
rs13119041	0.86[GIH][hapmap]
rs13148849	0.81[ASN][1000 genomes]
rs1352433	0.80[ASN][1000 genomes]
rs1352434	0.83[ASN][1000 genomes]
rs1472967	0.95[JPT][hapmap]
rs1507865	0.82[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs1586540	0.81[ASN][1000 genomes]
rs16861305	0.84[EUR][1000 genomes]
rs17656040	0.84[CHB][hapmap]
rs17656094	0.82[CHB][hapmap]
rs1876469	0.86[GIH][hapmap]
rs1948167	0.81[ASN][1000 genomes]
rs2102397	0.84[GIH][hapmap]
rs2291474	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2291475	0.95[JPT][hapmap]
rs2353314	0.83[ASN][1000 genomes]
rs2353315	0.90[ASN][1000 genomes]
rs2354348	0.84[GIH][hapmap]
rs28470767	0.86[GIH][hapmap]
rs34975258	0.90[ASN][1000 genomes]
rs35758434	0.81[ASN][1000 genomes]
rs3828496	0.81[ASN][1000 genomes]
rs392187	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs404445	0.95[JPT][hapmap]
rs411261	0.95[JPT][hapmap]
rs421833	0.95[JPT][hapmap]
rs4536901	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4694895	0.81[ASN][1000 genomes]
rs4695391	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs62311296	0.81[EUR][1000 genomes]
rs6447634	0.81[ASN][1000 genomes]
rs6447640	0.82[EUR][1000 genomes]
rs6811148	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs6816010	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs6821277	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6829716	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6836632	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs6843340	0.84[GIH][hapmap]
rs6848073	0.95[JPT][hapmap]
rs7438704	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs7438713	0.95[EUR][1000 genomes]
rs7654770	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7667288	0.86[GIH][hapmap]
rs7672892	0.80[ASN][1000 genomes]
rs7678379	0.89[GIH][hapmap];0.81[JPT][hapmap]
rs7697851	0.89[GIH][hapmap];0.81[JPT][hapmap]
rs776584	0.82[CHB][hapmap]
rs776591	0.82[CHB][hapmap]
rs796555	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs923372	0.81[ASN][1000 genomes]
rs923373	0.81[ASN][1000 genomes]
rs9291323	0.80[ASN][1000 genomes]
rs937888	0.82[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs937889	0.82[CHB][hapmap]
rs974014	0.81[ASN][1000 genomes]
rs974015	0.81[ASN][1000 genomes]
rs992423	0.89[GIH][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv1005268	chr4:48444307-48484389	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv537086	chr4:48444307-48484389	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6838613	SLC10A4	cis	lung	GTEx
rs6838613	OCIAD1	cis	Esophagus Muscularis	GTEx
rs6838613	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48473000-48482000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48473000-48483600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:48473600-48479400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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