Variant report

Variant	rs1894115
Chromosome Location	chr11:102176404-102176405
allele	A/C
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	FOXA1	chr11:102176121-102176472	A549	lung:	n/a	n/a
2	POLR2A	chr11:102175943-102177774	MCF10A-Er-Src	breast:	n/a	n/a
3	TFAP2C	chr11:102176379-102177854	Hela-S3	cervix:	n/a	n/a
4	MAFF	chr11:102176395-102176822	HepG2	liver:	n/a	chr11:102176579-102176593 chr11:102176580-102176598
5	MAFK	chr11:102176403-102176815	HepG2	liver:	n/a	chr11:102176576-102176596 chr11:102176581-102176596 chr11:102176579-102176593 chr11:102176578-102176594
6	POLR2A	chr11:102175716-102178596	MCF10A-Er-Src	breast:	n/a	n/a
7	TFAP2A	chr11:102176385-102177941	Hela-S3	cervix:	n/a	chr11:102177099-102177114
8	MAFK	chr11:102176191-102178133	Hela-S3	cervix:	n/a	chr11:102176576-102176596 chr11:102176581-102176596 chr11:102176579-102176593 chr11:102176578-102176594

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102175561..102178536-chr11:102186960..102189576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270868	TF binding region
ENSG00000023445	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10501998	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10501999	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225201	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225202	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11225203	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600522	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602147	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606268	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12098902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12280343	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576911	0.90[ASN][1000 genomes]
rs12787745	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12789170	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12794196	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17763827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17763887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17769417	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17878708	0.93[ASN][1000 genomes]
rs1894113	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894114	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408344	0.86[ASN][1000 genomes]
rs2511293	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511295	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604526	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604527	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604533	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2846848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2846849	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2846857	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2846858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852879	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2852880	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2852882	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852891	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3132831	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35612369	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58277500	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61893629	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480738	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924744	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928663	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7931341	0.92[ASN][1000 genomes]
rs7938790	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9665961	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh 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	11 gene(s)	inside rSNPs	diseases
6	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	10 gene(s)	inside rSNPs	diseases
7	esv3514195	chr11:102118479-102348362	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	esv3514197	chr11:102118479-102348362	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv975125	chr11:102175161-102176624	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1894115	CNTN5	cis	cerebellum	SCAN
rs1894115	C11orf70	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102170000-102176600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr11:102173200-102182400	Weak transcription	Gastric	stomach
3	chr11:102173600-102176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:102173600-102183800	Weak transcription	Lung	lung
5	chr11:102174200-102176800	Enhancers	Primary B cells from cord blood	blood
6	chr11:102174400-102177000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr11:102174400-102178400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr11:102174400-102178400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr11:102174600-102176600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:102174800-102176600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:102174800-102177400	Enhancers	Primary T cells from cord blood	blood
12	chr11:102174800-102178400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr11:102174800-102179600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr11:102175000-102176600	Weak transcription	Spleen	Spleen
15	chr11:102175200-102179800	Enhancers	Primary B cells from peripheral blood	blood
16	chr11:102175400-102176600	Enhancers	HMEC	breast
17	chr11:102175400-102177000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr11:102175400-102178400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:102175400-102178400	Enhancers	Fetal Thymus	thymus
20	chr11:102175600-102178200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:102175600-102178800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:102175800-102176800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr11:102175800-102176800	Weak transcription	Small Intestine	intestine
24	chr11:102176000-102176600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:102176000-102176800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr11:102176000-102177800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:102176000-102178000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:102176000-102178000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:102176000-102178400	Enhancers	Stomach Mucosa	stomach
30	chr11:102176200-102178200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:102176200-102178600	Enhancers	Primary hematopoietic stem cells	blood
32	chr11:102176400-102176600	Enhancers	Brain Angular Gyrus	brain
33	chr11:102176400-102176600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr11:102176400-102176800	Flanking Active TSS	A549	lung
35	chr11:102176400-102177000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:102176400-102177000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:102176400-102177000	Enhancers	Brain Cingulate Gyrus	brain
38	chr11:102176400-102177000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr11:102176400-102177600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr11:102176400-102177800	Enhancers	Brain Hippocampus Middle	brain
41	chr11:102176400-102177800	Enhancers	Fetal Intestine Small	intestine
42	chr11:102176400-102178200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr11:102176400-102178200	Enhancers	Fetal Intestine Large	intestine
44	chr11:102176400-102178200	Enhancers	HepG2	liver
45	chr11:102176400-102178400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:102176400-102178400	Enhancers	Placenta	Placenta
47	chr11:102176400-102178400	Enhancers	Thymus	Thymus
48	chr11:102176400-102178400	Flanking Active TSS	Dnd41	blood
49	chr11:102176400-102178400	Flanking Active TSS	Hela-S3	cervix
50	chr11:102176400-102178400	Enhancers	HSMM	muscle

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