Variant report

Variant	rs10838747
Chromosome Location	chr11:47716324-47716325
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47716027-47716401	K562	blood:	n/a	n/a

Variant related genes	Relation type
AGBL2	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10128705	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039308	0.86[ASN][1000 genomes]
rs11039324	0.85[ASN][1000 genomes]
rs11039342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039348	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039355	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039389	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039390	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039391	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039416	0.81[ASN][1000 genomes]
rs11039426	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11602339	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11602395	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11604825	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11605774	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823949	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12361031	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12363232	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12418852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12419507	0.85[ASN][1000 genomes]
rs12419692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12421210	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785833	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12787330	0.84[ASN][1000 genomes]
rs12787646	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12798346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12799623	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12803191	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34128973	0.81[ASN][1000 genomes]
rs34910028	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34923397	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34958982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs35805829	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35902101	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35985502	0.81[ASN][1000 genomes]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752797	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752873	0.81[ASN][1000 genomes]
rs56400411	0.82[AMR][1000 genomes]
rs59360790	0.89[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs7120333	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7130758	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928842	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10838747	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838747	SPI1	cis	multi-tissue	Pritchard
rs10838747	C1QTNF4	cis	Whole Blood	GTEx
rs10838747	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs10838747	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs10838747	FNBP4	cis	lesional skin	skin_eQTL
rs10838747	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs10838747	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs10838747	C1QTNF4	cis	lung	GTEx
rs10838747	Hs.6637	cis	multi-tissue	Pritchard
rs10838747	C1QTNF4	cis	multi-tissue	Pritchard
rs10838747	C1QTNF4	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47705600-47735600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47712000-47736000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:47712400-47723800	Weak transcription	Liver	Liver

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