Variant report

Variant	rs17707198
Chromosome Location	chr15:52573572-52573573
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr15:52573029-52573739	HepG2	liver:	n/a	n/a
2	RXRA	chr15:52573268-52573725	HepG2	liver:	n/a	n/a
3	CHD2	chr15:52573366-52573753	HepG2	liver:	n/a	n/a
4	MAZ	chr15:52573412-52573657	HepG2	liver:	n/a	n/a
5	HA-E2F1	chr15:52573187-52574195	MCF-7	breast:	n/a	n/a
6	RAD21	chr15:52573264-52573637	HepG2	liver:	n/a	n/a
7	FOXA2	chr15:52573263-52573954	HepG2	liver:	n/a	n/a
8	EP300	chr15:52573152-52573767	HepG2	liver:	n/a	n/a
9	RXRA	chr15:52573265-52573713	HepG2	liver:	n/a	n/a
10	MBD4	chr15:52573236-52573893	HepG2	liver:	n/a	n/a
11	TBP	chr15:52573337-52574013	HepG2	liver:	n/a	n/a
12	MXI1	chr15:52573276-52573710	HepG2	liver:	n/a	n/a
13	HNF4A	chr15:52573392-52573715	HepG2	liver:	n/a	n/a
14	FOXA1	chr15:52573376-52573712	T-47D	breast:	n/a	n/a
15	EP300	chr15:52572893-52573705	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:52573403-52573723	HepG2	liver:	n/a	n/a
17	TEAD4	chr15:52573160-52573768	HepG2	liver:	n/a	n/a
18	CEBPB	chr15:52573423-52573970	HepG2	liver:	n/a	n/a
19	ARID3A	chr15:52573363-52573870	HepG2	liver:	n/a	n/a
20	NFIC	chr15:52573136-52573700	HepG2	liver:	n/a	n/a
21	FOXA1	chr15:52573239-52573996	HepG2	liver:	n/a	n/a
22	NR2F2	chr15:52573147-52573927	HepG2	liver:	n/a	n/a
23	FOXA1	chr15:52573245-52573943	HepG2	liver:	n/a	n/a
24	RCOR1	chr15:52573129-52573648	HepG2	liver:	n/a	n/a
25	HDAC2	chr15:52573305-52573869	HepG2	liver:	n/a	n/a
26	RAD21	chr15:52573293-52573700	HepG2	liver:	n/a	n/a
27	NFIC	chr15:52573246-52573693	HepG2	liver:	n/a	n/a
28	MYBL2	chr15:52572804-52573779	HepG2	liver:	n/a	n/a
29	RAD21	chr15:52573195-52573734	HepG2	liver:	n/a	n/a
30	HDAC2	chr15:52573249-52573756	HepG2	liver:	n/a	n/a
31	HNF4A	chr15:52573295-52573710	HepG2	liver:	n/a	n/a
32	SP1	chr15:52573227-52573674	HepG2	liver:	n/a	chr15:52573403-52573412
33	HNF4G	chr15:52573329-52573680	HepG2	liver:	n/a	n/a
34	MYC	chr15:52573438-52573672	HepG2	liver:	n/a	n/a
35	MAX	chr15:52573364-52573576	HepG2	liver:	n/a	n/a
36	EP300	chr15:52573339-52573711	HepG2	liver:	n/a	n/a
37	FOXA1	chr15:52573291-52573723	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:52573228..52575829-chr15:52858890..52861430,2	MCF-7	breast:
2	chr15:52567021..52571873-chr15:52572571..52576998,5	MCF-7	breast:
3	chr15:52572320..52574802-chr15:52575555..52577846,2	MCF-7	breast:
4	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:

No data

Variant related genes	Relation type
MIR1266	TF binding region
ENSG00000128833	Chromatin interaction
ENSG00000221052	Chromatin interaction
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10851510	1.00[CEU][hapmap]
rs10851511	1.00[CEU][hapmap]
rs11070886	0.89[CHB][hapmap]
rs11070890	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3794551	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs4432216	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4496072	1.00[CEU][hapmap]
rs4514621	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4774617	1.00[CEU][hapmap]
rs4776031	1.00[CEU][hapmap]
rs59056894	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7165256	0.84[JPT][hapmap]
rs7172236	1.00[CEU][hapmap]
rs8025608	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
3	chr15:52553200-52575400	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
6	chr15:52555200-52580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52555400-52574400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:52555400-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:52555800-52574000	Weak transcription	Brain Anterior Caudate	brain
10	chr15:52555800-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:52555800-52576400	Weak transcription	Hela-S3	cervix
12	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:52557000-52575800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:52558200-52575400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr15:52558800-52579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:52559200-52573800	Weak transcription	Esophagus	oesophagus
17	chr15:52559400-52580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:52561400-52580600	Weak transcription	Spleen	Spleen
19	chr15:52563800-52575000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:52564400-52575800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:52565000-52575000	Strong transcription	Fetal Stomach	stomach
22	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
23	chr15:52567200-52575800	Strong transcription	Fetal Intestine Small	intestine
24	chr15:52568600-52576400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:52568600-52579400	Weak transcription	Stomach Mucosa	stomach
26	chr15:52568800-52580000	Weak transcription	Colonic Mucosa	Colon
27	chr15:52570800-52573600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:52570800-52580800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:52571200-52581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:52571400-52580600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:52571400-52580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:52571600-52573600	Weak transcription	A549	lung
35	chr15:52571600-52579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:52571600-52579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:52571800-52573800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:52571800-52574400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:52571800-52574800	Weak transcription	Adipose Nuclei	Adipose
40	chr15:52572200-52574200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:52572200-52575800	Enhancers	Pancreas	Pancrea
42	chr15:52572200-52577600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:52572400-52577000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:52572600-52573800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:52572800-52573800	Flanking Active TSS	HepG2	liver
46	chr15:52572800-52574000	Enhancers	Right Ventricle	heart
47	chr15:52572800-52574000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr15:52572800-52574400	Enhancers	Liver	Liver
49	chr15:52572800-52574400	Enhancers	Fetal Heart	heart
50	chr15:52572800-52574600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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