Variant report

Variant	rs12787013
Chromosome Location	chr11:5647719-5647720
allele	A/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	CEBPB	chr11:5647261-5647745	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:5644901-5647851	GM12891	blood:	n/a	n/a
3	FOS	chr11:5647407-5647778	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr11:5647408-5647740	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr11:5647441-5647722	A549	lung:	n/a	n/a
6	CEBPB	chr11:5647397-5647774	IMR90	lung:	n/a	n/a
7	FOS	chr11:5647387-5647769	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr11:5647414-5647753	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:5642318..5644325-chr11:5646414..5649300,2	MCF-7	breast:
2	chr11:5647376..5651052-chr11:5666185..5670181,3	K562	blood:
3	chr11:5638568..5642695-chr11:5644713..5649067,4	K562	blood:

Variant related genes	Relation type
ENSG00000239920	TF binding region
ENSG00000258659	Chromatin interaction
ENSG00000196565	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4910830	1.00[ASW][hapmap]

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	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1048455	chr11:5609783-5655393	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv896947	chr11:5631972-5659680	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12787013	OR51B4	cis	parietal	SCAN
rs12787013	CNGA4	cis	cerebellum	SCAN
rs12787013	ZNF215	cis	cerebellum	SCAN
rs12787013	UBQLNL	cis	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5640600-5651600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:5646200-5653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:5646400-5648200	Enhancers	Spleen	Spleen
4	chr11:5646800-5648800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:5647000-5648000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr11:5647000-5648600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:5647000-5648600	Enhancers	Placenta	Placenta
8	chr11:5647000-5648800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr11:5647000-5649000	Enhancers	Primary B cells from peripheral blood	blood
10	chr11:5647000-5649200	Weak transcription	Right Atrium	heart
11	chr11:5647000-5649600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:5647000-5653600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:5647000-5653600	Weak transcription	Left Ventricle	heart
14	chr11:5647000-5655200	Weak transcription	Fetal Thymus	thymus
15	chr11:5647000-5655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:5647000-5666800	Weak transcription	Fetal Brain Male	brain
17	chr11:5647000-5698800	Weak transcription	Colonic Mucosa	Colon
18	chr11:5647200-5649400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:5647200-5653600	Weak transcription	Fetal Lung	lung
20	chr11:5647200-5655000	Weak transcription	Small Intestine	intestine
21	chr11:5647200-5655600	Weak transcription	NHLF	lung
22	chr11:5647400-5647800	Enhancers	Primary B cells from cord blood	blood
23	chr11:5647400-5647800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr11:5647400-5647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:5647400-5647800	Enhancers	Fetal Intestine Small	intestine
26	chr11:5647400-5648000	Enhancers	Lung	lung
27	chr11:5647400-5648400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:5647400-5648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:5647400-5648800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr11:5647400-5649400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:5647400-5649800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr11:5647400-5650000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr11:5647400-5653400	Weak transcription	Fetal Muscle Leg	muscle
34	chr11:5647400-5653600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:5647400-5653600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:5647400-5653600	Weak transcription	Fetal Stomach	stomach
37	chr11:5647400-5653600	Weak transcription	Ovary	ovary
38	chr11:5647400-5653600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:5647400-5654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:5647400-5654600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:5647400-5654600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr11:5647400-5654600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:5647400-5654800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:5647400-5655000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:5647400-5655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:5647400-5655400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:5647400-5663000	Weak transcription	Aorta	Aorta
48	chr11:5647400-5663000	Weak transcription	Gastric	stomach
49	chr11:5647400-5663000	Weak transcription	Thymus	Thymus
50	chr11:5647400-5663400	Weak transcription	Esophagus	oesophagus

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