Variant report

Variant	rs60411293
Chromosome Location	chr1:45248202-45248203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr1:45242766-45248217	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:45247776-45248592	A549	lung:	n/a	n/a
7	POLR2A	chr1:45245085-45249976	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:45248075-45248500	K562	blood:	n/a	n/a
9	POLR2A	chr1:45240539-45248722	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr1:45245305-45248679	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:45239662-45248685	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	chr1:45194298..45199848-chr1:45247467..45253056,11	MCF-7	breast:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45193566..45196499-chr1:45246618..45248474,2	MCF-7	breast:
5	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
6	chr1:45246411..45248469-chr1:45275602..45279033,3	MCF-7	breast:

No data

Variant related genes	Relation type
RPS15AP11	TF binding region
ENSG00000173846	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000117425	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17883044	1.00[AMR][1000 genomes]
rs25687	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57175012	1.00[AMR][1000 genomes]
rs6656623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7515879	0.94[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	chr1:45243400-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:45243600-45249000	Strong transcription	Primary B cells from cord blood	blood
3	chr1:45243600-45249400	Weak transcription	Right Atrium	heart
4	chr1:45244000-45249000	Weak transcription	Fetal Lung	lung
5	chr1:45244000-45249800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:45244000-45249800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:45244200-45249000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:45244200-45249400	Weak transcription	Fetal Brain Male	brain
9	chr1:45244200-45249400	Strong transcription	Fetal Intestine Small	intestine
10	chr1:45244600-45248600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:45244600-45249200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:45244600-45249400	Weak transcription	Psoas Muscle	Psoas
13	chr1:45244600-45251600	Weak transcription	Small Intestine	intestine
14	chr1:45244800-45248600	Strong transcription	Fetal Thymus	thymus
15	chr1:45244800-45249000	Weak transcription	Fetal Heart	heart
16	chr1:45244800-45249000	Weak transcription	NHDF-Ad	bronchial
17	chr1:45244800-45249200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:45244800-45249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:45244800-45249400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:45244800-45249400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:45244800-45249400	Weak transcription	Fetal Kidney	kidney
22	chr1:45244800-45249400	Weak transcription	Stomach Mucosa	stomach
23	chr1:45245000-45249000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:45245000-45249400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:45245000-45249400	Weak transcription	Brain Substantia Nigra	brain
26	chr1:45245000-45249400	Weak transcription	NH-A	brain
27	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
28	chr1:45245200-45249200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:45245200-45249400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:45245200-45249400	Weak transcription	Gastric	stomach
31	chr1:45245600-45249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:45245600-45249600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:45245800-45249000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:45246000-45249400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:45246200-45249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:45246200-45249000	Weak transcription	HepG2	liver
37	chr1:45246400-45249400	Weak transcription	Aorta	Aorta
38	chr1:45246400-45251400	Weak transcription	HSMMtube	muscle
39	chr1:45246600-45249000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:45246600-45249200	Weak transcription	Brain Anterior Caudate	brain
41	chr1:45246600-45249400	Weak transcription	HMEC	breast
42	chr1:45246800-45249200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:45246800-45249200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:45247000-45248800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:45247000-45249200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:45247000-45249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:45247000-45249400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:45247000-45249400	Weak transcription	Osteobl	bone
49	chr1:45247200-45249000	Weak transcription	Lung	lung
50	chr1:45247200-45249200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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