Variant report

Variant	rs71324991
Chromosome Location	chr3:49759370-49759371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 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	chr3:49758190-49762295	A549	lung:	n/a	n/a
3	POLR2A	chr3:49754469-49762505	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:49757717-49759415	SK-N-SH	brain:	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	chr3:49757873-49762519	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49754970-49763587	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:49758785-49760594	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:49759367-49760535	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:49757798-49760188	K562	blood:	n/a	n/a
12	POLR2A	chr3:49757923-49759433	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49759193-49759560	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:49757760-49765712	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:49759350-49759375	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:49758881-49759586	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:49759106-49760086	K562	blood:	n/a	n/a
18	POLR2A	chr3:49755382-49762475	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:49757686-49761996	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr3:49757676-49762669	K562	blood:	n/a	n/a
21	POLR2A	chr3:49757898-49759505	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:49757768-49760063	U87	brain:	n/a	n/a
23	POLR2A	chr3:49758291-49759466	K562	blood:	n/a	n/a
24	POLR2A	chr3:49757795-49760139	GM19193	blood:	n/a	n/a
25	POLR2A	chr3:49757653-49762558	U87	brain:	n/a	n/a
26	POLR2A	chr3:49752889-49762689	GM12892	blood:	n/a	n/a
27	POLR2A	chr3:49758065-49762291	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr3:49759105-49762420	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:49757964-49759378	GM18505	blood:	n/a	n/a
30	POLR2A	chr3:49757757-49762595	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:49758270-49759468	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr3:49757849-49763169	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:49757775-49759748	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:49757724-49762442	HL-60	blood:	n/a	n/a
35	POLR2A	chr3:49757731-49761986	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:49757641-49760392	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr3:49759050-49759725	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr3:49754271-49762558	U87	brain:	n/a	n/a
39	POLR2A	chr3:49755615-49759711	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr3:49754554-49762400	K562	blood:	n/a	n/a
41	POLR2A	chr3:49757757-49760104	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:49757757-49760073	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr3:49757951-49760021	HEK293	kidney:	n/a	n/a
44	POLR2A	chr3:49757911-49762130	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:49757616-49759816	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr3:49757695-49761085	K562	blood:	n/a	n/a
47	POLR2A	chr3:49754384-49762352	GM12891	blood:	n/a	n/a
48	POLR2A	chr3:49759230-49759490	A549	lung:	n/a	n/a
49	POLR2A	chr3:49757748-49760551	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr3:49757605-49759527	HUVEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49758598..49759428-chr5:130506085..130506631,2	Hela-S3	cervix:
2	chr3:49758578..49761116-chr3:49892581..49894496,2	MCF-7	breast:
3	chr3:49725817..49728685-chr3:49758847..49761125,3	K562	blood:
4	chr3:49759227..49762200-chr3:49837244..49838747,2	MCF-7	breast:

No data

Variant related genes	Relation type
AMIGO3	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000187492	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000183763	Chromatin interaction
ENSG00000186687	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3356841	chr3:49758498-49761296	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr3:49753600-49759400	Weak transcription	K562	blood
5	chr3:49757000-49759800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:49757200-49760000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49757200-49760200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49757200-49760400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:49757200-49760400	Weak transcription	Psoas Muscle	Psoas
10	chr3:49757200-49760400	Weak transcription	Small Intestine	intestine
11	chr3:49757400-49759600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:49757400-49759800	Strong transcription	NHLF	lung
13	chr3:49757400-49760000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:49757400-49760000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:49757400-49760000	Weak transcription	Right Atrium	heart
16	chr3:49757400-49760200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:49757400-49760200	Weak transcription	Fetal Kidney	kidney
18	chr3:49757400-49760600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:49757600-49759600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:49757600-49759800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:49757600-49759800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:49757600-49759800	Genic enhancers	Dnd41	blood
23	chr3:49757600-49760200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:49757600-49760200	Weak transcription	Fetal Heart	heart
25	chr3:49757800-49759400	Strong transcription	Lung	lung
26	chr3:49757800-49759600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:49757800-49759600	Strong transcription	GM12878-XiMat	blood
28	chr3:49757800-49759800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:49757800-49759800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:49757800-49759800	Strong transcription	Fetal Stomach	stomach
31	chr3:49757800-49759800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr3:49757800-49760000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:49757800-49760000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:49757800-49760000	Weak transcription	Fetal Brain Male	brain
35	chr3:49757800-49760000	Strong transcription	Fetal Thymus	thymus
36	chr3:49757800-49760000	Genic enhancers	Stomach Mucosa	stomach
37	chr3:49757800-49760200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:49757800-49760200	Strong transcription	Fetal Intestine Small	intestine
39	chr3:49758000-49759600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:49758000-49759600	Strong transcription	Liver	Liver
41	chr3:49758000-49759600	Genic enhancers	Gastric	stomach
42	chr3:49758000-49759600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:49758000-49759800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:49758000-49759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:49758000-49759800	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:49758000-49759800	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr3:49758000-49759800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:49758000-49759800	Strong transcription	A549	lung
49	chr3:49758000-49760000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:49758000-49760000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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