Variant report

Variant	rs12526935
Chromosome Location	chr6:119373912-119373913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11967399	0.83[ASN][1000 genomes]
rs11967889	0.83[ASN][1000 genomes]
rs1413906	0.99[ASN][1000 genomes]
rs1570493	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17513308	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1762200	0.86[ASN][1000 genomes]
rs1775619	0.82[CHB][hapmap]
rs2051056	0.82[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap]
rs2051057	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs2295709	0.82[CHB][hapmap]
rs2357020	0.82[ASN][1000 genomes]
rs2357030	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs2782575	0.85[ASN][1000 genomes]
rs2797352	0.84[ASN][1000 genomes]
rs284919	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2884078	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4946383	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs4946388	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4946389	0.99[ASN][1000 genomes]
rs4946390	0.99[ASN][1000 genomes]
rs57100274	0.81[ASN][1000 genomes]
rs57285368	0.83[ASN][1000 genomes]
rs6929403	0.95[JPT][hapmap]
rs6931558	0.98[ASN][1000 genomes]
rs706978	0.82[CHB][hapmap]
rs7756475	0.99[ASN][1000 genomes]
rs7764418	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs794260	0.88[ASN][1000 genomes]
rs794261	0.86[ASN][1000 genomes]
rs794262	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs794263	0.86[ASN][1000 genomes]
rs794264	0.86[ASN][1000 genomes]
rs794266	0.86[ASN][1000 genomes]
rs794614	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs808028	0.99[ASN][1000 genomes]
rs813812	0.88[ASN][1000 genomes]
rs9374777	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9387624	0.89[JPT][hapmap]
rs9387629	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387630	0.98[ASN][1000 genomes]
rs9398499	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401113	0.83[ASN][1000 genomes]
rs9401118	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481881	0.99[ASN][1000 genomes]
rs954753	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12526935	MCM9	cis	parietal	SCAN
rs12526935	C6orf204	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119373000-119375800	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr6:119373200-119374200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:119373200-119374600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:119373200-119375000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr6:119373400-119374400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:119373400-119374400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:119373400-119374800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:119373400-119374800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:119373400-119374800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:119373400-119375200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:119373400-119375800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:119373600-119374000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:119373600-119374000	Enhancers	Brain Anterior Caudate	brain
14	chr6:119373600-119374400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:119373600-119374600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr6:119373600-119374800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr6:119373600-119375200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:119373600-119375800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:119373800-119374200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr6:119373800-119374600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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