Variant report

Variant	rs6898203
Chromosome Location	chr5:179503416-179503417
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10051694	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs10056991	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs10071652	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs10903247	0.86[TSI][hapmap]
rs11249664	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs11249665	1.00[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs11739898	0.86[JPT][hapmap]
rs11750102	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs17681274	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs2083967	0.94[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs2278662	0.81[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs3776946	0.89[CEU][hapmap]
rs4700852	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4700864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6601077	0.84[CEU][hapmap];0.92[CHB][hapmap]
rs6862105	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6869349	0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6873317	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6873639	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6884565	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7725201	0.95[CEU][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs7734329	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs9329095	0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6898203	C5orf45	cis	parietal	SCAN
rs6898203	LTC4S	cis	cerebellum	SCAN
rs6898203	CLTB	cis	parietal	SCAN
rs6898203	TRIM7	cis	parietal	SCAN
rs6898203	C21orf128	trans	parietal	SCAN
rs6898203	RASGEF1C	cis	parietal	SCAN
rs6898203	RASGEF1C	cis	cerebellum	SCAN
rs6898203	PROP1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179499600-179508200	Weak transcription	Right Ventricle	heart
3	chr5:179500200-179506800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:179502200-179507600	Enhancers	Liver	Liver
5	chr5:179502800-179506800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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