Variant report

Variant	rs7515879
Chromosome Location	chr1:45247354-45247355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45243922-45247518	U87	brain:	n/a	n/a
2	POLR2A	chr1:45243842-45247542	A549	lung:	n/a	n/a
3	POLR2A	chr1:45240631-45247540	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45240526-45248028	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:45245714-45248113	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:45245136-45247601	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:45245731-45247484	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:45240483-45248016	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:45242580-45247462	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:45245435-45247654	Hela-S3	cervix:	n/a	n/a
12	PML	chr1:45245762-45247403	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:45245767-45247689	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr1:45245270-45247449	K562	blood:	n/a	n/a
17	STAT5A	chr1:45246555-45247378	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:45246261-45247391	IMR90	lung:	n/a	n/a
19	POLR2A	chr1:45245246-45247630	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:45246468-45247472	NB4	blood:	n/a	n/a
21	POLR2A	chr1:45242766-45248217	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:45246266-45247608	U87	brain:	n/a	n/a
23	POLR2A	chr1:45242928-45247383	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:45245346-45248048	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:45245990-45247391	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:45245249-45247425	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:45245234-45247606	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:45245680-45247542	HCT-116	colon:	n/a	n/a
30	POLR2A	chr1:45246265-45247434	GM18505	blood:	n/a	n/a
31	POLR2A	chr1:45245563-45247412	Hela-S3	cervix:	n/a	n/a
32	HEY1	chr1:45245582-45247381	HepG2	liver:	n/a	n/a
33	NFATC1	chr1:45246956-45247476	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:45245886-45247549	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr1:45240713-45247745	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr1:45243853-45247621	U87	brain:	n/a	n/a
37	POLR2A	chr1:45245340-45247541	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:45240271-45247480	K562	blood:	n/a	n/a
39	POLR2A	chr1:45245085-45249976	PANC-1	pancreas:	n/a	n/a
40	BCL3	chr1:45246376-45247474	A549	lung:	n/a	n/a
41	POLR2A	chr1:45239953-45247379	K562	blood:	n/a	n/a
42	MTA3	chr1:45246585-45247476	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:45240502-45248124	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:45245598-45247607	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr1:45245677-45248089	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr1:45245541-45247575	MCF-7	breast:	n/a	n/a
47	POLR2A	chr1:45240539-45248722	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr1:45240524-45248015	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:45245305-45248679	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr1:45245333-45247464	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45246917..45250948-chr1:45965225..45967473,3	K562	blood:
2	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
3	chr1:45193566..45196499-chr1:45246618..45248474,2	MCF-7	breast:
4	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
5	chr1:45246411..45248469-chr1:45275602..45279033,3	MCF-7	breast:
6	chr1:45245131..45247941-chr1:45805894..45808200,2	K562	blood:

No data

Variant related genes	Relation type
RPS15AP11	TF binding region
ENSG00000173846	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11573597	1.00[MEX][hapmap]
rs11573600	1.00[MEX][hapmap]
rs17883044	1.00[AMR][1000 genomes]
rs25687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3903059	1.00[MEX][hapmap]
rs57175012	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60411293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690913	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
12	nsv945912	chr1:45243841-45248516	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45242600-45247600	Strong transcription	Brain Hippocampus Middle	brain
2	chr1:45242800-45247400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:45242800-45247800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:45243200-45247400	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:45243400-45247400	Strong transcription	Liver	Liver
6	chr1:45243400-45248200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:45243400-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:45243600-45247400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr1:45243600-45247400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:45243600-45247400	Strong transcription	Esophagus	oesophagus
11	chr1:45243600-45248000	Strong transcription	Fetal Brain Female	brain
12	chr1:45243600-45248200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:45243600-45249000	Strong transcription	Primary B cells from cord blood	blood
14	chr1:45243600-45249400	Weak transcription	Right Atrium	heart
15	chr1:45243800-45248000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:45244000-45247400	Strong transcription	Colonic Mucosa	Colon
17	chr1:45244000-45249000	Weak transcription	Fetal Lung	lung
18	chr1:45244000-45249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:45244000-45249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:45244200-45247400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:45244200-45247400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:45244200-45247400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:45244200-45247400	Strong transcription	Thymus	Thymus
24	chr1:45244200-45247400	Strong transcription	HSMM	muscle
25	chr1:45244200-45247400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:45244200-45247600	Strong transcription	Primary T cells from cord blood	blood
27	chr1:45244200-45247600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:45244200-45247600	Strong transcription	Right Ventricle	heart
29	chr1:45244200-45248200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:45244200-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:45244200-45249400	Weak transcription	Fetal Brain Male	brain
32	chr1:45244200-45249400	Strong transcription	Fetal Intestine Small	intestine
33	chr1:45244600-45247400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:45244600-45247400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:45244600-45247400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:45244600-45247400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:45244600-45247400	Strong transcription	Brain Germinal Matrix	brain
38	chr1:45244600-45247400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:45244600-45247400	Strong transcription	Dnd41	blood
40	chr1:45244600-45247600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:45244600-45247600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:45244600-45248000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:45244600-45248200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:45244600-45248200	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:45244600-45248200	Strong transcription	Fetal Stomach	stomach
46	chr1:45244600-45248600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:45244600-45249200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:45244600-45249400	Weak transcription	Psoas Muscle	Psoas
49	chr1:45244600-45251600	Weak transcription	Small Intestine	intestine
50	chr1:45244800-45247400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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