Variant report

Variant	rs1792773
Chromosome Location	chr11:104972190-104972191
allele	C/T
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	FOS	chr11:104971878-104972346	MCF10A-Er-Src	breast:	n/a	chr11:104971936-104971945
2	MYC	chr11:104971795-104972416	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr11:104972038-104972480	MCF10A-Er-Src	breast:	n/a	chr11:104972173-104972184
4	STAT3	chr11:104972055-104972356	MCF10A-Er-Src	breast:	n/a	chr11:104972173-104972184
5	MYC	chr11:104971999-104972414	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr11:104972042-104972303	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr11:104972085-104972366	MCF10A-Er-Src	breast:	n/a	chr11:104972173-104972184
8	FOS	chr11:104972012-104972419	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr11:104972036-104972353	MCF10A-Er-Src	breast:	n/a	chr11:104972173-104972184
10	POLR2A	chr11:104970868-104972388	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr11:104971940-104972376	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr11:104971978-104972500	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CARD17	TF binding region
CASP1	TF binding region
CARD16	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10895769	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1483025	0.90[ASN][1000 genomes]
rs1503399	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1503400	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1623342	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1628434	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1630085	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1699073	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1699078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1699080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1699081	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs1699082	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1699083	0.89[ASN][1000 genomes]
rs1699084	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1699086	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1699087	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1699088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699095	0.92[ASN][1000 genomes]
rs1785864	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs1785872	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1785873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1785878	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1785882	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1792752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792753	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1792757	0.94[ASN][1000 genomes]
rs1792763	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap]
rs1792764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792766	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792770	0.99[ASN][1000 genomes]
rs1792771	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1847293	0.94[ASN][1000 genomes]
rs2062806	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2174158	0.96[ASN][1000 genomes]
rs2852987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736149	0.90[ASN][1000 genomes]
rs4534547	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs472886	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs484345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs489753	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508337	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs529809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs531589	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs572717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7932543	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7934144	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046098	chr11:104207210-105003661	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	esv2757475	chr11:104895876-104979717	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv2759863	chr11:104895876-104979717	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1042388	chr11:104934347-104988325	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
11	esv2756562	chr11:104937371-104981568	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
12	nsv1040275	chr11:104939029-104988325	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
13	nsv8871	chr11:104941750-104973508	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
14	nsv1054109	chr11:104948117-104976058	Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
15	nsv949337	chr11:104950007-105510193	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1049355	chr11:104950412-104972518	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
17	nsv442241	chr11:104950424-104972558	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
18	esv2762941	chr11:104952282-104972558	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
19	nsv524985	chr11:104960997-104991640	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
20	esv3425474	chr11:104962498-104978307	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
21	nsv975977	chr11:104971009-104972355	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1792773	CARD17	cis	Esophagus Mucosa	GTEx
rs1792773	INCA	cis	multi-tissue	Pritchard
rs1792773	C11orf70	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104969600-104972200	Enhancers	NHEK	skin
2	chr11:104970000-104974200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:104970200-104972200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr11:104970200-104972200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr11:104970400-104972200	Enhancers	Primary hematopoietic stem cells	blood
6	chr11:104970400-104972200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:104970400-104972400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:104970400-104972600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr11:104970600-104972200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:104970600-104972200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr11:104970800-104972200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:104970800-104972400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr11:104971000-104972200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:104971000-104972200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr11:104971000-104972200	Enhancers	Adipose Nuclei	Adipose
16	chr11:104971000-104972200	Enhancers	Placenta	Placenta
17	chr11:104971000-104972400	Active TSS	Duodenum Mucosa	Duodenum
18	chr11:104971200-104972400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr11:104971400-104972200	Active TSS	Primary T cells fromperipheralblood	blood
20	chr11:104971600-104972400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:104971600-104972400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:104971600-104972400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:104971800-104972200	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr11:104972000-104972200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:104972000-104972200	Enhancers	Esophagus	oesophagus

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