Variant report

Variant	rs73398513
Chromosome Location	chr15:41059785-41059786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41057635-41061953	K562	blood:	n/a	n/a
2	POLR2A	chr15:41057608-41059993	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr15:41059282-41059803	HepG2	liver:	n/a	n/a
4	CCNT2	chr15:41059739-41059798	K562	blood:	n/a	n/a
5	POLR2A	chr15:41055973-41059813	K562	blood:	n/a	n/a
6	POLR2A	chr15:41059733-41059991	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:41057591-41062786	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:41059117-41059953	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:41059074-41061819	K562	blood:	n/a	n/a
10	HCFC1	chr15:41054658-41062813	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr15:41059083-41060095	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:41059107-41059839	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:41059478-41059798	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
2	chr15:41059265..41060152-chr5:168006202..168006986,2	Hela-S3	cervix:
3	chr15:41058103..41060724-chr15:41061996..41063790,2	MCF-7	breast:
4	chr15:41059314..41061862-chr15:41077543..41079580,2	K562	blood:
5	chr15:41047666..41050190-chr15:41058981..41061979,2	MCF-7	breast:
6	chr15:41054628..41058503-chr15:41058814..41065530,15	K562	blood:
7	chr15:41055716..41060288-chr15:41072655..41077591,4	MCF-7	breast:

No data

Variant related genes	Relation type
C15orf62	TF binding region
ENSG00000104129	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000120137	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000137880	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16971001	1.00[ASN][1000 genomes]
rs2016546	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301176	0.94[ASN][1000 genomes]
rs2898999	1.00[ASN][1000 genomes]
rs3784290	1.00[ASN][1000 genomes]
rs57096780	1.00[ASN][1000 genomes]
rs57272245	1.00[ASN][1000 genomes]
rs7174651	1.00[ASN][1000 genomes]
rs7175221	1.00[ASN][1000 genomes]
rs7179899	1.00[ASN][1000 genomes]
rs73398545	1.00[ASN][1000 genomes]
rs8025558	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029321	1.00[ASN][1000 genomes]
rs8031526	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 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	chr15:41057000-41059800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr15:41057000-41060000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr15:41057000-41060200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:41057000-41062200	Weak transcription	Aorta	Aorta
5	chr15:41057000-41062600	Enhancers	NH-A	brain
6	chr15:41057200-41059800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr15:41057200-41059800	Weak transcription	Brain Substantia Nigra	brain
8	chr15:41057200-41060000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr15:41057200-41061200	Weak transcription	Right Atrium	heart
10	chr15:41057200-41063200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41057200-41063400	Weak transcription	HSMMtube	muscle
12	chr15:41057200-41063800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:41057200-41065400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:41057200-41068200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:41057400-41061200	Weak transcription	Fetal Brain Male	brain
16	chr15:41057400-41063200	Enhancers	Stomach Mucosa	stomach
17	chr15:41057400-41070800	Weak transcription	Psoas Muscle	Psoas
18	chr15:41057600-41059800	Genic enhancers	Liver	Liver
19	chr15:41057600-41060000	Weak transcription	Small Intestine	intestine
20	chr15:41057600-41062600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:41057600-41063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:41057600-41066600	Weak transcription	Fetal Heart	heart
23	chr15:41057600-41067400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:41057800-41059800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:41057800-41060800	Weak transcription	Primary T cells from cord blood	blood
26	chr15:41057800-41063200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:41058000-41059800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:41058000-41060200	Weak transcription	Primary B cells from cord blood	blood
29	chr15:41058000-41060600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr15:41058000-41060800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:41058000-41060800	Transcr. at gene 5' and 3'	Hela-S3	cervix
32	chr15:41058000-41061200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:41058000-41063400	Weak transcription	Left Ventricle	heart
34	chr15:41058000-41069000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:41058200-41060000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:41058200-41060200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:41058200-41060800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr15:41058200-41061200	Genic enhancers	Fetal Intestine Large	intestine
39	chr15:41058200-41066800	Weak transcription	Fetal Kidney	kidney
40	chr15:41058200-41067400	Weak transcription	A549	lung
41	chr15:41058400-41060000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr15:41058400-41060600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:41058400-41060600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:41058400-41060600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr15:41058400-41061000	Genic enhancers	Fetal Intestine Small	intestine
46	chr15:41058400-41061200	Strong transcription	Fetal Stomach	stomach
47	chr15:41058400-41068800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:41058600-41060000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:41058600-41060200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:41058600-41060200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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