Variant report

Variant	rs10838738
Chromosome Location	chr11:47663049-47663050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:47662891-47664597	IMR90	lung:	n/a	n/a
2	MYC	chr11:47662599-47665236	K562	blood:	n/a	chr11:47664084-47664093 chr11:47665218-47665227 chr11:47665219-47665226 chr11:47665213-47665228 chr11:47665216-47665227
3	POLR2A	chr11:47662956-47664626	HUVEC	blood vessel:	n/a	n/a
4	MXI1	chr11:47662753-47664743	SK-N-SH	brain:	n/a	n/a
5	E2F4	chr11:47662993-47663193	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr11:47663015-47664547	Hela-S3	cervix:	n/a	n/a
7	HCFC1	chr11:47662559-47665501	Hela-S3	cervix:	n/a	n/a
8	MYC	chr11:47662762-47663413	MCF10A-Er-Src	breast:	n/a	n/a
9	SIN3A	chr11:47663038-47664659	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47660129..47661788-chr11:47662493..47664105,2	MCF-7	breast:
2	chr11:47599184..47601918-chr11:47661794..47664226,4	MCF-7	breast:
3	chr11:47661932..47663606-chr11:47755819..47758646,2	K562	blood:
4	chr11:47660831..47663188-chr11:47962801..47965480,2	K562	blood:
5	chr11:47663042..47663543-chr12:109536619..109537119,2	Hela-S3	cervix:
6	chr11:47206285..47208872-chr11:47661768..47663771,2	K562	blood:
7	chr11:47572750..47576231-chr11:47662956..47665605,3	K562	blood:
8	chr11:47661534..47663358-chr11:47740296..47742508,2	K562	blood:
9	chr11:47662615..47664358-chr11:47788211..47790386,2	K562	blood:
10	chr11:47599811..47601701-chr11:47661212..47663329,2	K562	blood:
11	chr11:47599811..47601393-chr11:47661829..47664063,2	K562	blood:
12	chr11:47662583..47667763-chr11:47735291..47739208,6	MCF-7	breast:
13	chr11:47662615..47665881-chr11:47786940..47791485,8	K562	blood:
14	chr11:47662579..47666117-chr11:47735408..47738256,8	MCF-7	breast:

No data

Variant related genes	Relation type
MTCH2	TF binding region
ENSG00000109920	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000109919	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000165923	Chromatin interaction
ENSG00000231880	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000123444	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 23 )

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

rs_ID	r²[population]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838747	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[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.82[ASN][1000 genomes]
rs11039308	0.96[ASN][1000 genomes]
rs11039324	0.91[ASN][1000 genomes]
rs11039342	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039348	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039355	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11602339	0.81[AMR][1000 genomes]
rs11602395	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11604825	0.81[ASN][1000 genomes]
rs12363232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419507	0.91[ASN][1000 genomes]
rs12419692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12421210	0.81[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787646	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12798028	0.83[ASN][1000 genomes]
rs12798346	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12799623	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12803191	0.81[ASN][1000 genomes]
rs1317149	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2030166	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs34910028	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34923397	0.80[ASN][1000 genomes]
rs34958982	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56400411	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59360790	0.95[ASN][1000 genomes]
rs66749409	0.84[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7927771	1.00[CEU][hapmap]
rs7928842	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]

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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	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
3	esv3424537	chr11:47660545-47663980	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Body mass index	19079261	GWAS catalog

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs10838738	C1QTNF4	cis	multi-tissue	Pritchard
rs10838738	C1QTNF4	cis	lung	GTEx
rs10838738	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10838738	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838738	Hs.6637	cis	multi-tissue	Pritchard
rs10838738	C1QTNF4	cis	Whole Blood	GTEx
rs10838738	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs10838738	MTCH2	cis	multi-tissue	Pritchard
rs10838738	C1QTNF4	cis	Artery Tibial	GTEx
rs10838738	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs10838738	C1QTNF4	cis	Muscle Skeletal	GTEx
rs10838738	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs10838738	ACP2	cis	lymphoblastoid	seeQTL
rs10838738	SPI1	cis	lymphoblastoid	seeQTL
rs10838738	PSMC3	cis	cerebellum	SCAN
rs10838738	SLC35C1	cis	parietal	SCAN
rs10838738	CUGBP1	cis	Liver	GTEx
rs10838738	MYBPC3	cis	multi-tissue	Pritchard
rs10838738	MADD	cis	cerebellum	SCAN
rs10838738	SPI1	cis	multi-tissue	Pritchard
rs10838738	MTCH2	cis	cerebellum	SCAN
rs10838738	C1QTNF4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47637600-47663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47648200-47663200	Weak transcription	Gastric	stomach
3	chr11:47657000-47663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:47657000-47663200	Weak transcription	Esophagus	oesophagus
5	chr11:47657200-47663400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:47658800-47663200	Weak transcription	Lung	lung
7	chr11:47661200-47663200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:47661400-47663200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr11:47661400-47663200	Weak transcription	Placenta	Placenta
10	chr11:47661800-47663200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:47662000-47663200	Enhancers	Small Intestine	intestine
12	chr11:47662000-47663600	Flanking Active TSS	Liver	Liver
13	chr11:47662200-47663200	Enhancers	Primary B cells from peripheral blood	blood
14	chr11:47662200-47663200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr11:47662200-47663200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:47662200-47663200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:47662200-47663200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr11:47662200-47663200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:47662200-47663200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:47662200-47663200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr11:47662200-47663400	Flanking Active TSS	Hela-S3	cervix
22	chr11:47662400-47663200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:47662400-47663200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:47662400-47663200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr11:47662400-47663200	Flanking Active TSS	HMEC	breast
26	chr11:47662400-47663200	Flanking Active TSS	NHEK	skin
27	chr11:47662400-47663400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:47662400-47663400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr11:47662400-47663400	Enhancers	Spleen	Spleen
30	chr11:47662400-47663400	Flanking Active TSS	Dnd41	blood
31	chr11:47662400-47664800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:47662400-47664800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr11:47662600-47663200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:47662600-47663200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr11:47662600-47663200	Enhancers	Primary hematopoietic stem cells	blood
36	chr11:47662600-47663200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr11:47662600-47663200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr11:47662600-47663200	Enhancers	Fetal Muscle Trunk	muscle
39	chr11:47662600-47663400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr11:47662600-47663400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:47662600-47663400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr11:47662600-47663400	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr11:47662600-47663600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr11:47662600-47663600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr11:47662600-47663600	Flanking Active TSS	Osteobl	bone
46	chr11:47662600-47663800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr11:47662600-47664600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:47662600-47664600	Active TSS	HSMM	muscle
49	chr11:47662600-47664800	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr11:47662800-47663200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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