Variant report

Variant	rs7634945
Chromosome Location	chr3:49758111-49758112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49757537-49762490	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49754469-49762505	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:49757717-49759415	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr3:49757690-49758945	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:49757841-49761975	PBDE	blood:	n/a	n/a
6	POLR2A	chr3:49755286-49762590	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr3:49757627-49758822	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:49758111-49758847	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:49757873-49762519	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:49754970-49763587	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49757939-49758883	K562	blood:	n/a	n/a
12	POLR2A	chr3:49757798-49760188	K562	blood:	n/a	n/a
13	POLR2A	chr3:49757923-49759433	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:49757896-49758122	A549	lung:	n/a	n/a
15	POLR2A	chr3:49757849-49759240	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:49757760-49765712	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:49757971-49758871	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:49757632-49759077	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:49757899-49759232	GM18526	blood:	n/a	n/a
20	POU2F2	chr3:49757744-49758348	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:49755382-49762475	MCF-7	breast:	n/a	n/a
22	POLR2A	chr3:49757686-49761996	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:49757888-49758191	HCT-116	colon:	n/a	n/a
24	POLR2A	chr3:49757676-49762669	K562	blood:	n/a	n/a
25	POLR2A	chr3:49757729-49759041	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:49757898-49759505	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:49757768-49760063	U87	brain:	n/a	n/a
28	POLR2A	chr3:49757859-49758966	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr3:49757795-49760139	GM19193	blood:	n/a	n/a
30	POLR2A	chr3:49755367-49758782	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:49757653-49762558	U87	brain:	n/a	n/a
32	POLR2A	chr3:49757667-49758835	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:49752889-49762689	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:49758065-49762291	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:49757912-49758895	GM19099	blood:	n/a	n/a
36	POLR2A	chr3:49757964-49759378	GM18505	blood:	n/a	n/a
37	POLR2A	chr3:49758049-49758620	K562	blood:	n/a	n/a
38	POLR2A	chr3:49757757-49762595	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:49757826-49758856	Raji	blood:	n/a	n/a
40	POLR2A	chr3:49757849-49763169	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr3:49757775-49759748	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:49757724-49762442	HL-60	blood:	n/a	n/a
43	POLR2A	chr3:49757757-49759348	SK-N-MC	brain:	n/a	n/a
44	PML	chr3:49757732-49758202	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:49758093-49758609	MCF-7	breast:	n/a	n/a
46	PBX3	chr3:49755730-49759087	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr3:49757731-49761986	GM12878	blood:	n/a	n/a
48	MTA3	chr3:49757594-49758845	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:49757641-49760392	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr3:49754271-49762558	U87	brain:	n/a	n/a

No data

Variant related genes	Relation type
AMIGO3	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs34379671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34630302	1.00[AMR][1000 genomes]
rs35481257	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6772424	1.00[AMR][1000 genomes]
rs6797615	1.00[AMR][1000 genomes]
rs6800591	1.00[AMR][1000 genomes]
rs6806073	1.00[AMR][1000 genomes]
rs6808633	1.00[AMR][1000 genomes]
rs72938200	1.00[AMR][1000 genomes]
rs7615240	1.00[AMR][1000 genomes]
rs7616171	1.00[AMR][1000 genomes]
rs7623582	1.00[AMR][1000 genomes]
rs7626820	1.00[AMR][1000 genomes]
rs7633189	1.00[AMR][1000 genomes]
rs7636222	1.00[AMR][1000 genomes]
rs7637266	1.00[AMR][1000 genomes]
rs7641976	1.00[AMR][1000 genomes]
rs7648632	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1796605	chr3:49744556-49760567	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49740600-49759800	Weak transcription	Hela-S3	cervix
2	chr3:49752600-49759800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:49753000-49759600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49753600-49758200	Weak transcription	HepG2	liver
5	chr3:49753600-49759400	Weak transcription	K562	blood
6	chr3:49757000-49759800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:49757200-49758200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:49757200-49758200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:49757200-49758200	Enhancers	Pancreas	Pancrea
10	chr3:49757200-49758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:49757200-49758400	Weak transcription	HSMM	muscle
12	chr3:49757200-49760000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:49757200-49760200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:49757200-49760400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:49757200-49760400	Weak transcription	Psoas Muscle	Psoas
16	chr3:49757200-49760400	Weak transcription	Small Intestine	intestine
17	chr3:49757400-49758200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:49757400-49758200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:49757400-49758200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:49757400-49758200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:49757400-49758200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:49757400-49758200	Weak transcription	Primary B cells from cord blood	blood
23	chr3:49757400-49758200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:49757400-49758200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:49757400-49758200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:49757400-49758200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:49757400-49758200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:49757400-49758200	Weak transcription	Esophagus	oesophagus
29	chr3:49757400-49758200	Weak transcription	Fetal Lung	lung
30	chr3:49757400-49758200	Weak transcription	Left Ventricle	heart
31	chr3:49757400-49758200	Weak transcription	Ovary	ovary
32	chr3:49757400-49758200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:49757400-49758200	Weak transcription	Thymus	Thymus
34	chr3:49757400-49758200	Weak transcription	HUVEC	blood vessel
35	chr3:49757400-49758400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:49757400-49758400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:49757400-49758400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:49757400-49758400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:49757400-49758400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:49757400-49758400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:49757400-49758400	Weak transcription	HMEC	breast
42	chr3:49757400-49758400	Weak transcription	HSMMtube	muscle
43	chr3:49757400-49759600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:49757400-49759800	Strong transcription	NHLF	lung
45	chr3:49757400-49760000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:49757400-49760000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:49757400-49760000	Weak transcription	Right Atrium	heart
48	chr3:49757400-49760200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:49757400-49760200	Weak transcription	Fetal Kidney	kidney
50	chr3:49757400-49760600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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