Variant report

Variant	rs9401118
Chromosome Location	chr6:119374749-119374750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119374505..119375317-chr8:134874073..134874573,2	K562	blood:
2	chr6:119374401..119377359-chr6:119388791..119390597,2	K562	blood:

Variant related genes	Relation type
ENSG00000207982	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11967399	0.83[ASN][1000 genomes]
rs11967889	0.83[ASN][1000 genomes]
rs12526935	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342794	0.85[EUR][1000 genomes]
rs1413906	0.99[ASN][1000 genomes]
rs1570493	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17513308	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1762200	0.86[ASN][1000 genomes]
rs1775619	0.82[CHB][hapmap]
rs1935817	0.87[ASW][hapmap];0.91[YRI][hapmap]
rs2051056	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	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2782575	0.85[ASN][1000 genomes]
rs2797352	0.84[ASN][1000 genomes]
rs284919	0.83[CHB][hapmap]
rs2884078	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946383	0.88[CHB][hapmap]
rs4946388	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	0.92[AMR][1000 genomes];0.95[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9387624	0.89[JPT][hapmap]
rs9387629	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387630	0.98[ASN][1000 genomes]
rs9398499	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401113	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9401118	MCM9	cis	parietal	SCAN
rs9401118	ASF1A	Cis_1M	lymphoblastoid	RTeQTL
rs9401118	C6orf204	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 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	chr6:119373200-119375000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr6:119373400-119374800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr6:119373400-119374800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr6:119373400-119374800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:119373400-119375200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:119373400-119375800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:119373600-119374800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr6:119373600-119375200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:119373600-119375800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:119374400-119375000	Enhancers	Cortex derived primary cultured neurospheres	brain

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