Variant report

Variant	rs11558739
Chromosome Location	chr14:39648629-39648630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:39648334-39648664	K562	blood:	n/a	n/a
2	POLR2A	chr14:39648024-39648814	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:39642960-39651251	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr14:39648606-39649092	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr14:39648182-39648752	K562	blood:	n/a	n/a
6	HEY1	chr14:39646033-39648837	HepG2	liver:	n/a	n/a
7	POLR2A	chr14:39647907-39648816	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr14:39647911-39648724	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:39643051-39648902	HepG2	liver:	n/a	n/a
10	POLR2A	chr14:39643261-39648811	K562	blood:	n/a	n/a
11	HEY1	chr14:39647913-39648856	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:39647197-39648901	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:39648448-39648708	MCF-7	breast:	n/a	n/a
14	POLR2A	chr14:39648122-39648799	A549	lung:	n/a	n/a
15	POLR2A	chr14:39647370-39648850	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39632209..39634394-chr14:39648466..39651233,2	K562	blood:
2	chr14:39647303..39649184-chr14:39736283..39738077,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259083	TF binding region
ENSG00000150527	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10459481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483542	0.81[YRI][hapmap]
rs10872915	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11620885	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11620889	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11622021	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12184985	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12432236	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs12432764	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12433305	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434282	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12435383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12436766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17616038	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs17616116	0.91[YRI][hapmap]
rs17678595	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17678780	0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs1884385	0.92[CEU][hapmap];0.84[YRI][hapmap]
rs1964841	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2273316	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2415534	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34417819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35802696	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57049071	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57120608	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61999361	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61999428	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61999432	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999433	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61999439	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999443	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999444	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61999445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62000580	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7157388	0.84[CEU][hapmap]
rs7158043	0.83[AMR][1000 genomes]
rs72673310	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs761808	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9322995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39645400-39649000	Genic enhancers	Primary T cells fromperipheralblood	blood
2	chr14:39645600-39655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr14:39645800-39651200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr14:39645800-39653000	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr14:39645800-39653400	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr14:39645800-39654600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr14:39645800-39655200	Strong transcription	Placenta	Placenta
8	chr14:39645800-39657200	Strong transcription	HSMM	muscle
9	chr14:39646000-39651400	Strong transcription	Fetal Kidney	kidney
10	chr14:39646000-39652800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr14:39646000-39654200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr14:39646000-39654800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr14:39646000-39654800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:39646000-39655200	Strong transcription	HSMMtube	muscle
15	chr14:39646200-39648800	Strong transcription	Ovary	ovary
16	chr14:39646200-39651000	Strong transcription	Esophagus	oesophagus
17	chr14:39646200-39651600	Genic enhancers	HUVEC	blood vessel
18	chr14:39646200-39652600	Strong transcription	Brain Anterior Caudate	brain
19	chr14:39646200-39653000	Strong transcription	Fetal Lung	lung
20	chr14:39646200-39654400	Strong transcription	Primary B cells from cord blood	blood
21	chr14:39646200-39654400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:39646200-39654400	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr14:39646200-39654600	Strong transcription	Osteobl	bone
24	chr14:39646200-39654800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:39646200-39654800	Strong transcription	Fetal Brain Female	brain
26	chr14:39646200-39655000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr14:39646400-39648800	Strong transcription	Spleen	Spleen
28	chr14:39646400-39648800	Genic enhancers	A549	lung
29	chr14:39646400-39649000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr14:39646400-39649400	Weak transcription	Fetal Heart	heart
31	chr14:39646400-39649600	Weak transcription	Stomach Mucosa	stomach
32	chr14:39646400-39649800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr14:39646400-39649800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:39646400-39650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr14:39646400-39651200	Strong transcription	Colonic Mucosa	Colon
36	chr14:39646400-39651200	Strong transcription	Rectal Smooth Muscle	rectum
37	chr14:39646400-39652600	Strong transcription	Brain Hippocampus Middle	brain
38	chr14:39646400-39653000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr14:39646400-39653000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr14:39646400-39653400	Strong transcription	NHDF-Ad	bronchial
41	chr14:39646400-39654200	Strong transcription	Brain Substantia Nigra	brain
42	chr14:39646400-39654400	Strong transcription	NHLF	lung
43	chr14:39646400-39654800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:39646400-39654800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr14:39646400-39654800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:39646400-39655000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr14:39646400-39655000	Strong transcription	HMEC	breast
48	chr14:39646400-39655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr14:39646400-39655200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr14:39646400-39655200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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