Variant report

Variant	rs61370152
Chromosome Location	chr3:49199521-49199522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49199197-49200017	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr3:49198774-49199996	K562	blood:	n/a	n/a
3	POLR2A	chr3:49198751-49201892	HL-60	blood:	n/a	n/a
4	POLR2A	chr3:49198739-49201514	K562	blood:	n/a	n/a
5	POLR2A	chr3:49198510-49204140	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:49198712-49199868	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:49198544-49200023	GM12891	blood:	n/a	n/a
8	USF2	chr3:49199501-49199918	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:49198599-49199917	U87	brain:	n/a	n/a
10	POLR2A	chr3:49199397-49199774	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:49199166-49199814	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:49198676-49199863	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:49199384-49199813	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49199446-49199951	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:49198535-49201959	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:49198772-49199892	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:49199368-49199792	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:49198905-49200016	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr3:49198769-49200074	HL-60	blood:	n/a	n/a
20	POLR2A	chr3:49199053-49199879	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:49199287-49199557	U87	brain:	n/a	n/a
22	SPI1	chr3:49199493-49200035	HL-60	blood:	n/a	n/a
23	POLR2A	chr3:49198483-49199914	GM12892	blood:	n/a	n/a
24	RUNX3	chr3:49199249-49199568	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:49199397-49199852	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:49197955-49203552	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr3:49199327-49199819	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:49199407-49199829	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr3:49198616-49200008	K562	blood:	n/a	n/a
30	POLR2A	chr3:49199007-49199985	GM12891	blood:	n/a	n/a
31	POLR2A	chr3:49199225-49200865	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:49198739-49201658	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:49198961-49199827	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:49199254-49199557	U87	brain:	n/a	n/a
35	POLR2A	chr3:49199506-49199710	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr3:49198670-49199943	GM12891	blood:	n/a	n/a
37	POLR2A	chr3:49198555-49199614	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:49198678-49199911	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:49199349-49199526	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:49198512-49204161	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:49199269-49199887	U87	brain:	n/a	n/a
42	POLR2A	chr3:49198105-49200990	K562	blood:	n/a	n/a
43	POLR2A	chr3:49199241-49199891	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:49199031-49200014	HCT-116	colon:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49197673..49199686-chr3:49449232..49451070,2	K562	blood:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49168509..49171088-chr3:49198215..49200498,3	K562	blood:
4	chr3:49067951..49070552-chr3:49199245..49201626,2	K562	blood:
5	chr3:49166454..49167956-chr3:49197730..49200400,2	K562	blood:
6	chr3:49198168..49200645-chr3:49211215..49212732,2	K562	blood:
7	chr3:49057940..49060006-chr3:49197956..49200673,2	MCF-7	breast:
8	chr3:49199406..49201947-chr3:49447942..49450781,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270441	TF binding region
ENSG00000185909	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000145022	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs58625868	1.00[AMR][1000 genomes]
rs73833527	1.00[AMR][1000 genomes]
rs7650868	1.00[AMR][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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49191000-49199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
4	chr3:49195000-49199600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:49195200-49200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:49195200-49202400	Weak transcription	Fetal Kidney	kidney
7	chr3:49195400-49200400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:49195600-49200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:49195600-49200200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:49195600-49200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49195600-49200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:49195600-49200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:49195600-49200400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:49195600-49202200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:49195800-49199600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49196000-49202400	Strong transcription	Fetal Stomach	stomach
17	chr3:49196200-49200200	Weak transcription	Fetal Lung	lung
18	chr3:49196400-49200400	Weak transcription	HepG2	liver
19	chr3:49196400-49202200	Weak transcription	Right Atrium	heart
20	chr3:49196600-49200400	Weak transcription	HSMMtube	muscle
21	chr3:49196600-49200600	Weak transcription	NHDF-Ad	bronchial
22	chr3:49196600-49200800	Weak transcription	Hela-S3	cervix
23	chr3:49196800-49200200	Weak transcription	Left Ventricle	heart
24	chr3:49196800-49200200	Weak transcription	HMEC	breast
25	chr3:49197000-49200000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:49197200-49200200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:49197200-49200200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:49197400-49199600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:49197400-49199800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:49197400-49201000	Weak transcription	K562	blood
31	chr3:49197600-49200200	Weak transcription	Liver	Liver
32	chr3:49197600-49200400	Weak transcription	Colonic Mucosa	Colon
33	chr3:49197800-49200000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:49197800-49200200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:49197800-49200400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:49197800-49200400	Weak transcription	Osteobl	bone
37	chr3:49198000-49199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:49198000-49199600	Weak transcription	GM12878-XiMat	blood
39	chr3:49198000-49200400	Weak transcription	HUVEC	blood vessel
40	chr3:49198000-49201800	Strong transcription	Thymus	Thymus
41	chr3:49198000-49202200	Weak transcription	Small Intestine	intestine
42	chr3:49198000-49202400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49198200-49200400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:49198200-49201600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:49198200-49201600	Strong transcription	Aorta	Aorta
46	chr3:49198200-49201600	Strong transcription	Brain Germinal Matrix	brain
47	chr3:49198200-49202000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:49198200-49202000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:49198200-49202200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:49198200-49202200	Strong transcription	Fetal Brain Female	brain

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