Variant report

Variant	rs1785878
Chromosome Location	chr11:104963106-104963107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10895769	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483025	0.86[ASN][1000 genomes]
rs1503399	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1503400	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1623342	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628434	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630085	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1699073	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1699078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1699080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699081	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1699082	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1699083	0.92[ASN][1000 genomes]
rs1699084	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1699095	0.95[ASN][1000 genomes]
rs1785864	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs1785872	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1785873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1785876	0.80[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];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792753	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs1792755	0.80[ASN][1000 genomes]
rs1792756	0.80[ASN][1000 genomes]
rs1792757	0.98[ASN][1000 genomes]
rs1792763	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1792764	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792765	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792766	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792770	0.95[ASN][1000 genomes]
rs1792771	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792773	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]
rs1792777	0.80[ASN][1000 genomes]
rs1847293	0.90[ASN][1000 genomes]
rs2062806	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2174158	0.92[ASN][1000 genomes]
rs2852987	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736149	0.86[ASN][1000 genomes]
rs4534547	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4638280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs472886	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs484345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs489753	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508337	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs529809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs531589	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs562441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs572717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7932543	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7934144	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	esv3450730	chr11:104938956-104968986	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
13	nsv1040275	chr11:104939029-104988325	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
14	nsv8871	chr11:104941750-104973508	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island	4 gene(s)	inside rSNPs	diseases
15	esv33277	chr11:104944762-104969485	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
16	nsv1054109	chr11:104948117-104976058	Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
17	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
18	nsv1049355	chr11:104950412-104972518	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
19	nsv442241	chr11:104950424-104972558	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
20	esv2762941	chr11:104952282-104972558	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
21	esv3452067	chr11:104953416-104969855	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
22	nsv524985	chr11:104960997-104991640	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
23	nsv976502	chr11:104962087-104965143	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
24	esv3425474	chr11:104962498-104978307	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1785878	CARD17	cis	Esophagus Mucosa	GTEx
rs1785878	INCA	cis	multi-tissue	Pritchard
rs1785878	C11orf70	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:104962600-104963600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:104962800-104963600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr11:104962800-104964000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:104962800-104964400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:104963000-104963200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:104963000-104963200	Enhancers	NHEK	skin
7	chr11:104963000-104963400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:104963000-104963400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:104963000-104963400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:104963000-104964400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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