Variant report

Variant	rs11708811
Chromosome Location	chr3:52328607-52328608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52327536-52335341	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52328342-52328771	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:52328512-52328763	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:52328387-52328912	HepG2	liver:	n/a	n/a
6	HEY1	chr3:52328293-52328736	HepG2	liver:	n/a	n/a
7	HEY1	chr3:52327933-52329294	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52326795-52334549	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:52328355-52329117	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:52328430-52330742	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52327519-52329068	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:52326721-52333108	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52261084..52264395-chr3:52328500..52330625,3	K562	blood:
2	chr3:52328227..52330124-chr3:52332267..52334731,2	MCF-7	breast:
3	chr3:52261625..52264395-chr3:52328500..52330239,2	K562	blood:

No data

Variant related genes	Relation type
MIR135A1	TF binding region
ENSG00000173366	Chromatin interaction
ENSG00000242797	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.91[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706541	0.93[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs11711914	0.94[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714358	1.00[EUR][1000 genomes]
rs11715208	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715382	0.91[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs11717028	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.96[EUR][1000 genomes]
rs11719760	0.93[EUR][1000 genomes]
rs11720365	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11721277	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17052052	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs17052054	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs1769	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs35976326	1.00[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs3886875	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4082828	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs55676974	1.00[EUR][1000 genomes]
rs55806905	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55813842	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55847657	0.96[EUR][1000 genomes]
rs56002041	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56352611	0.96[EUR][1000 genomes]
rs56899118	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58531656	0.96[EUR][1000 genomes]
rs60382084	0.96[EUR][1000 genomes]
rs61644644	1.00[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	1.00[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs6809248	0.96[EUR][1000 genomes]
rs724801	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73072990	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73088773	0.97[EUR][1000 genomes]
rs73088783	0.96[EUR][1000 genomes]
rs73088785	0.96[EUR][1000 genomes]
rs73088791	1.00[EUR][1000 genomes]
rs73088800	0.96[EUR][1000 genomes]
rs73091166	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73091168	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615405	0.97[EUR][1000 genomes]
rs7628461	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7633687	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
10	esv3402579	chr3:52323712-52330410	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11708811	NISCH	cis	lymphoblastoid	seeQTL
rs11708811	DNAH1	cis	cerebellum	SCAN
rs11708811	TKT	cis	cerebellum	SCAN
rs11708811	SEMA3G	cis	cerebellum	SCAN
rs11708811	ZNF589	cis	cerebellum	SCAN
rs11708811	MST1	cis	parietal	SCAN
rs11708811	DNAH1	cis	parietal	SCAN
rs11708811	NISCH	cis	parietal	SCAN
rs11708811	PPM1M	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
4	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
11	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
12	chr3:52323600-52330400	Weak transcription	HSMM	muscle
13	chr3:52323800-52329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:52324000-52331800	Weak transcription	K562	blood
15	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:52324200-52331400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:52324400-52328800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52324400-52328800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:52324400-52329600	Strong transcription	Thymus	Thymus
20	chr3:52324400-52330200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:52324400-52331000	Strong transcription	Primary T cells from cord blood	blood
22	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:52324600-52329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:52324600-52329200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:52324600-52329400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:52324600-52329600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:52324600-52329600	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:52324600-52330200	Strong transcription	Placenta	Placenta
29	chr3:52324600-52330400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:52324600-52330600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:52324800-52329000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52324800-52329200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:52324800-52329200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:52325000-52328800	Strong transcription	Brain Substantia Nigra	brain
35	chr3:52325000-52328800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:52325000-52329200	Strong transcription	Primary B cells from cord blood	blood
37	chr3:52325000-52330200	Strong transcription	Brain Cingulate Gyrus	brain
38	chr3:52325000-52331200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:52325000-52332000	Strong transcription	Right Ventricle	heart
40	chr3:52325200-52328800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:52325200-52330800	Strong transcription	Spleen	Spleen
42	chr3:52325400-52329800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:52325400-52331200	Strong transcription	Fetal Stomach	stomach
44	chr3:52325600-52330200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:52325600-52330200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:52325600-52330600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:52325600-52331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:52325800-52330600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:52325800-52331200	Strong transcription	Rectal Mucosa Donor 29	rectum

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