Variant report

Variant	rs519380
Chromosome Location	chr11:66409409-66409410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66409292-66409817	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:66404758-66409916	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr11:66409368-66409889	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:66409330-66409778	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr11:66408926-66409903	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr11:66407452-66415502	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:66409280-66409919	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:66404694-66409669	GM12892	blood:	n/a	n/a
9	POLR2A	chr11:66409338-66409873	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66405952..66409597-chr11:66443012..66447533,6	MCF-7	breast:
2	chr11:66407180..66409474-chr11:66600961..66602936,2	K562	blood:
3	chr11:66407739..66410273-chr11:66444249..66447501,5	K562	blood:
4	chr11:66408468..66412282-chr11:66430332..66434495,4	K562	blood:
5	chr11:66409123..66411413-chr17:62289160..62291716,2	MCF-7	breast:
6	chr11:66283972..66286341-chr11:66409087..66411174,2	K562	blood:
7	chr11:66310423..66314650-chr11:66409018..66412449,5	K562	blood:
8	chr11:66358667..66365231-chr11:66403397..66409781,9	K562	blood:
9	chr11:66405423..66410273-chr11:66443859..66447584,9	K562	blood:

No data

Variant related genes	Relation type
RBM4	TF binding region
ENSG00000248746	Chromatin interaction
ENSG00000173992	Chromatin interaction
ENSG00000136478	Chromatin interaction
ENSG00000182791	Chromatin interaction
ENSG00000258297	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000173914	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10501397	0.93[MEX][hapmap]
rs11227499	0.93[MEX][hapmap]
rs11227501	0.93[MEX][hapmap]
rs11227515	0.93[MEX][hapmap]
rs11227527	0.93[MEX][hapmap]
rs11227596	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11550057	0.84[TSI][hapmap]
rs11550299	0.92[MEX][hapmap]
rs11821155	0.93[MEX][hapmap]
rs11822028	0.93[MEX][hapmap]
rs13897	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs15969	0.84[TSI][hapmap]
rs17065	1.00[CHB][hapmap]
rs17496250	1.00[CHB][hapmap]
rs2075792	0.81[CEU][hapmap]
rs2277302	0.93[MEX][hapmap]
rs2298806	0.93[MEX][hapmap]
rs2305535	0.93[MEX][hapmap]
rs3179961	0.93[MEX][hapmap]
rs3737525	1.00[CHB][hapmap];0.93[MEX][hapmap]
rs3741360	0.93[MEX][hapmap]
rs3782079	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3816492	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs3819247	0.92[MEX][hapmap]
rs3825065	0.93[MEX][hapmap]
rs3867133	0.88[TSI][hapmap]
rs3892818	0.93[MEX][hapmap]
rs4576	0.91[GIH][hapmap];0.93[MEX][hapmap]
rs4630309	0.91[GIH][hapmap]
rs477335	0.86[ASN][1000 genomes]
rs478807	0.82[ASN][1000 genomes]
rs4930183	0.87[CEU][hapmap]
rs4930378	0.93[MEX][hapmap]
rs4930379	0.93[MEX][hapmap]
rs527550	0.86[ASN][1000 genomes]
rs563344	0.88[ASN][1000 genomes]
rs573673	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs575797	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs623022	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs639938	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs645307	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs648491	0.82[ASN][1000 genomes]
rs7950407	0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs519380	ESRRA	cis	cerebellum	SCAN
rs519380	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs519380	CCND1	cis	parietal	SCAN
rs519380	SPTBN2	cis	cerebellum	SCAN
rs519380	CTSF	cis	parietal	SCAN
rs519380	CDC42EP2	cis	cerebellum	SCAN
rs519380	SART1	cis	cerebellum	SCAN
rs519380	CTSF	cis	cerebellum	SCAN
rs519380	UNC93B1	cis	cerebellum	SCAN
rs519380	PACS1	cis	parietal	SCAN
rs519380	CCS	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66406200-66410200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr11:66406200-66410400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr11:66406200-66410400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
4	chr11:66406200-66410600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr11:66406200-66411000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:66406600-66409800	Transcr. at gene 5' and 3'	K562	blood
7	chr11:66406600-66410400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:66406800-66410400	Transcr. at gene 5' and 3'	HMEC	breast
9	chr11:66406800-66410600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr11:66406800-66411200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:66406800-66411200	Transcr. at gene 5' and 3'	Fetal Lung	lung
12	chr11:66406800-66411800	Transcr. at gene 5' and 3'	HSMM	muscle
13	chr11:66406800-66413000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr11:66407000-66409600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
15	chr11:66407000-66409600	Transcr. at gene 5' and 3'	A549	lung
16	chr11:66407000-66409800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
17	chr11:66407000-66410000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:66407000-66410600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
19	chr11:66407000-66411600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
20	chr11:66407000-66411800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:66407000-66413600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
22	chr11:66407000-66434400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:66407200-66409800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
24	chr11:66407200-66409800	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr11:66407200-66409800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
26	chr11:66407200-66409800	Transcr. at gene 5' and 3'	Thymus	Thymus
27	chr11:66407200-66410200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
28	chr11:66407200-66410400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
29	chr11:66407200-66410400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
30	chr11:66407200-66410400	Transcr. at gene 5' and 3'	NHEK	skin
31	chr11:66407200-66411800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:66407200-66411800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
33	chr11:66407200-66413000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:66407200-66413000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr11:66407200-66413600	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr11:66407200-66413800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr11:66407400-66409600	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:66407400-66409600	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
39	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
40	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Liver	Liver
45	chr11:66407400-66409800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
46	chr11:66407400-66410000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:66407400-66410200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:66407400-66410200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
49	chr11:66407400-66410200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
50	chr11:66407400-66410400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose

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