Variant report

Variant	rs11669732
Chromosome Location	chr19:55912332-55912333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55909995-55912686	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:55912005-55912432	A549	lung:	n/a	n/a
3	POLR2A	chr19:55911771-55912650	A549	lung:	n/a	n/a
4	POLR2A	chr19:55910670-55912779	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:55909949-55912650	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:55911686-55912691	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:55910713-55912744	K562	blood:	n/a	n/a
8	POLR2A	chr19:55910129-55912674	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:55910031-55914597	GM12892	blood:	n/a	n/a
10	SIN3AK20	chr19:55911780-55912603	K562	blood:	n/a	n/a
11	POLR2A	chr19:55910771-55912609	K562	blood:	n/a	n/a
12	POLR2A	chr19:55911703-55912437	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:55910692-55912663	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:55910308-55912744	K562	blood:	n/a	n/a
15	POLR2A	chr19:55911706-55912650	ECC-1	luminal epithelium:	n/a	n/a
16	CCNT2	chr19:55912218-55912480	K562	blood:	n/a	n/a
17	GATA3	chr19:55910690-55912447	A549	lung:	n/a	n/a
18	POLR2A	chr19:55909545-55914730	U87	brain:	n/a	n/a
19	POLR2A	chr19:55911802-55912586	GM12878	blood:	n/a	n/a
20	BCL3	chr19:55909710-55912639	A549	lung:	n/a	n/a
21	JUND	chr19:55910735-55912590	HCT-116	colon:	n/a	n/a
22	POLR2A	chr19:55910738-55913366	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr19:55910739-55912557	GM18505	blood:	n/a	n/a
24	HEY1	chr19:55911616-55914690	K562	blood:	n/a	n/a
25	POLR2A	chr19:55910765-55912697	K562	blood:	n/a	n/a
26	BCL3	chr19:55910672-55912380	A549	lung:	n/a	n/a
27	POLR2A	chr19:55911704-55912852	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr19:55912155-55912361	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:55910308-55912620	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:55910121-55915188	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:55910765-55912601	K562	blood:	n/a	n/a
32	PBX3	chr19:55910754-55912534	A549	lung:	n/a	n/a
33	POLR2A	chr19:55910763-55912578	PBDE	blood:	n/a	n/a
34	POLR2A	chr19:55910728-55912664	HCT-116	colon:	n/a	n/a
35	POLR2A	chr19:55910832-55912573	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:55910754-55912680	HL-60	blood:	n/a	n/a
37	POLR2A	chr19:55911647-55912640	K562	blood:	n/a	n/a
38	POLR2A	chr19:55910743-55912681	HL-60	blood:	n/a	n/a
39	POLR2A	chr19:55910183-55912875	K562	blood:	n/a	n/a
40	POLR2A	chr19:55910665-55912611	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:55910101-55912701	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr19:55910736-55912591	HCT-116	colon:	n/a	n/a
43	POLR2A	chr19:55910751-55912647	GM12891	blood:	n/a	n/a
44	POLR2A	chr19:55911697-55912650	H1-hESC	embryonic stem cell:	n/a	n/a
45	HEY1	chr19:55911703-55912680	K562	blood:	n/a	n/a
46	POLR2A	chr19:55910669-55914680	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr19:55910741-55912662	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr19:55910140-55916359	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr19:55912229-55912380	A549	lung:	n/a	n/a
50	POLR2A	chr19:55910213-55912712	GM12892	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55910368..55912840-chr19:55964651..55967610,2	K562	blood:
2	chr19:55911623..55913706-chr19:55914461..55917038,2	MCF-7	breast:
3	chr19:55911367..55913938-chr19:55973377..55976304,2	K562	blood:
4	chr19:55812755..55814760-chr19:55911814..55913636,2	MCF-7	breast:
5	chr19:55769482..55772014-chr19:55910008..55913343,3	K562	blood:
6	chr19:55910844..55913006-chr19:55952542..55954951,2	K562	blood:
7	chr19:55909744..55913358-chr19:55997717..56001739,3	K562	blood:
8	chr19:55857803..55861096-chr19:55912151..55914962,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267093	TF binding region
ENSG00000179954	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000105063	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3810168	0.85[CHD][hapmap]
rs4806668	0.85[CHD][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	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11669732	VN1R1	cis	cerebellum	SCAN
rs11669732	ZNF776	cis	parietal	SCAN
rs11669732	ZNF444	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55899200-55913400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
3	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
4	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
5	chr19:55901200-55913200	Weak transcription	Small Intestine	intestine
6	chr19:55901600-55914400	Weak transcription	Fetal Kidney	kidney
7	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
8	chr19:55902200-55912400	Weak transcription	Colonic Mucosa	Colon
9	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:55903000-55913200	Weak transcription	Fetal Lung	lung
11	chr19:55903000-55914000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:55903400-55913000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:55903400-55913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:55904400-55913200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:55906000-55913600	Weak transcription	HepG2	liver
16	chr19:55910200-55917000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:55910800-55913400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:55910800-55917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:55910800-55917600	Strong transcription	Brain Anterior Caudate	brain
20	chr19:55911000-55915400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:55911000-55915800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:55911000-55917000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:55911000-55917000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr19:55911000-55917000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:55911000-55917000	Strong transcription	Fetal Intestine Large	intestine
26	chr19:55911000-55917000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr19:55911200-55912400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:55911200-55912400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:55911200-55913400	Strong transcription	Thymus	Thymus
30	chr19:55911200-55913800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:55911200-55914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:55911200-55914600	Strong transcription	Osteobl	bone
33	chr19:55911200-55915400	Strong transcription	Fetal Thymus	thymus
34	chr19:55911200-55915800	Strong transcription	Primary T cells from cord blood	blood
35	chr19:55911200-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:55911200-55917000	Strong transcription	Fetal Stomach	stomach
37	chr19:55911200-55917200	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:55911400-55912400	Weak transcription	Esophagus	oesophagus
39	chr19:55911400-55912600	Genic enhancers	Fetal Brain Female	brain
40	chr19:55911400-55913400	Strong transcription	Brain Germinal Matrix	brain
41	chr19:55911400-55915400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:55911400-55916000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:55911400-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:55911400-55917000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:55911600-55913600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:55911600-55915400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:55911600-55915400	Genic enhancers	A549	lung
48	chr19:55911600-55916000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:55911600-55916200	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr19:55911600-55916600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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