Variant report

Variant	rs11042463
Chromosome Location	chr11:9670404-9670405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10743115	0.90[ASN][1000 genomes]
rs10840278	0.92[ASN][1000 genomes]
rs10840280	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042458	0.91[ASN][1000 genomes]
rs11602208	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605234	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12275368	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12288440	0.81[ASN][1000 genomes]
rs12288444	0.89[ASN][1000 genomes]
rs12790033	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2082806	0.81[ASN][1000 genomes]
rs4910059	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6483580	0.87[ASN][1000 genomes]
rs7120033	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv896986	chr11:9636854-9679145	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv972945	chr11:9660423-9684250	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv521528	chr11:9667917-9672214	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv526210	chr11:9669363-9672214	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11042463	EIF3F	cis	cerebellum	SCAN
rs11042463	SWAP70	cis	multi-tissue	Pritchard
rs11042463	GVIN1	cis	cerebellum	SCAN
rs11042463	SWAP70	Cis_1M	lymphoblastoid	RTeQTL
rs11042463	CYB5R2	cis	parietal	SCAN
rs11042463	APBB1	cis	parietal	SCAN
rs11042463	MRPL17	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9668000-9673200	Weak transcription	Small Intestine	intestine
2	chr11:9668000-9673200	Weak transcription	Spleen	Spleen
3	chr11:9670000-9670600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr11:9670000-9670600	Enhancers	HSMMtube	muscle
5	chr11:9670000-9671200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:9670000-9671200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:9670000-9671400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr11:9670200-9671200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr11:9670400-9670600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr11:9670400-9670600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr11:9670400-9673000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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