Variant report

Variant	rs2388023
Chromosome Location	chr15:93442379-93442380
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93433692-93455675	K562	blood:	n/a	n/a
2	KAP1	chr15:93442294-93443141	K562	blood:	n/a	n/a
3	POLR2A	chr15:93441969-93442673	GM12891	blood:	n/a	n/a
4	RFX5	chr15:93442249-93443021	K562	blood:	n/a	n/a
5	POLR2A	chr15:93442056-93442785	GM12891	blood:	n/a	n/a
6	EP300	chr15:93442323-93444325	K562	blood:	n/a	chr15:93443079-93443093 chr15:93443654-93443670
7	POLR2A	chr15:93441964-93442528	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:93440318-93444999	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:93442026-93442619	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:93441946-93442731	GM12892	blood:	n/a	n/a
11	POLR2A	chr15:93441933-93442938	PANC-1	pancreas:	n/a	n/a
12	ARID3A	chr15:93441974-93445376	K562	blood:	n/a	n/a
13	POLR2A	chr15:93440733-93444962	A549	lung:	n/a	n/a
14	POLR2A	chr15:93442324-93442481	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:93442127-93442509	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:93442024-93442750	GM12892	blood:	n/a	n/a
17	POLR2A	chr15:93442080-93442729	HepG2	liver:	n/a	n/a
18	POLR2A	chr15:93442034-93443015	U87	brain:	n/a	n/a
19	POLR2A	chr15:93441953-93448610	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:93441370-93442561	K562	blood:	n/a	n/a
21	POLR2A	chr15:93441989-93442765	GM12891	blood:	n/a	n/a
22	POLR2A	chr15:93440648-93443934	K562	blood:	n/a	n/a
23	POLR2A	chr15:93442004-93442742	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:93441805-93445098	U87	brain:	n/a	n/a
25	TBL1XR1	chr15:93442055-93449323	K562	blood:	n/a	n/a
26	POLR2A	chr15:93442078-93445028	GM12891	blood:	n/a	n/a
27	POLR2A	chr15:93442125-93442501	U87	brain:	n/a	n/a
28	POLR2A	chr15:93441952-93442862	HepG2	liver:	n/a	n/a
29	CHD1	chr15:93442192-93453134	IMR90	lung:	n/a	chr15:93447634-93447644 chr15:93448003-93448013 chr15:93442831-93442841
30	RCOR1	chr15:93442244-93443903	IMR90	lung:	n/a	n/a
31	POLR2A	chr15:93441993-93442568	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:93442017-93442893	GM12892	blood:	n/a	n/a
33	POLR2A	chr15:93442201-93442460	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr15:93442082-93442602	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:93439531-93442863	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:93441804-93445254	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
2	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
3	chr15:93180068..93182597-chr15:93441905..93444737,2	MCF-7	breast:
4	chr15:93338780..93342194-chr15:93442202..93446226,4	MCF-7	breast:
5	chr15:93441494..93443862-chr3:43731000..43733877,2	MCF-7	breast:
6	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
7	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
8	chr15:93338607..93340953-chr15:93442127..93443801,2	MCF-7	breast:

No data

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000185442	Chromatin interaction
ENSG00000011198	Chromatin interaction
ENSG00000160746	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000258527	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11856160	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1881837	0.80[EUR][1000 genomes]
rs4778053	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62023121	0.83[EUR][1000 genomes]
rs6497005	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS 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	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv1851305	chr15:93429646-93446869	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93428600-93443600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:93429400-93442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:93430800-93443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:93431000-93442400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:93431600-93442800	Strong transcription	NHDF-Ad	bronchial
6	chr15:93431600-93443000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:93431800-93442800	Strong transcription	Osteobl	bone
8	chr15:93432000-93442400	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr15:93432600-93442400	Strong transcription	HUVEC	blood vessel
10	chr15:93432600-93442600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr15:93432600-93443200	Weak transcription	Right Atrium	heart
12	chr15:93433200-93442800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:93434600-93442600	Strong transcription	Placenta	Placenta
14	chr15:93435000-93442800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:93435000-93443200	Weak transcription	Stomach Mucosa	stomach
16	chr15:93436200-93443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:93436400-93443200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:93436400-93443200	Weak transcription	Ovary	ovary
19	chr15:93436600-93443200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:93436600-93443200	Weak transcription	Small Intestine	intestine
21	chr15:93436800-93442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:93437400-93443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:93437600-93443400	Weak transcription	Lung	lung
24	chr15:93437800-93443200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:93438000-93443000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:93438000-93443000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:93438000-93443200	Weak transcription	Colonic Mucosa	Colon
28	chr15:93438000-93443200	Weak transcription	Fetal Brain Male	brain
29	chr15:93438000-93443200	Weak transcription	HSMMtube	muscle
30	chr15:93438000-93443600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:93438200-93443000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:93438200-93443200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:93438200-93443200	Weak transcription	Right Ventricle	heart
34	chr15:93438200-93443200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:93438200-93443400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:93438200-93443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:93438200-93443400	Weak transcription	Esophagus	oesophagus
38	chr15:93438200-93444400	Weak transcription	Gastric	stomach
39	chr15:93438200-93447200	Weak transcription	Spleen	Spleen
40	chr15:93438400-93442400	Genic enhancers	Hela-S3	cervix
41	chr15:93438400-93442600	Strong transcription	Fetal Thymus	thymus
42	chr15:93438400-93442800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:93438400-93443200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:93438400-93443200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:93438400-93443200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:93438400-93443200	Weak transcription	Fetal Intestine Small	intestine
47	chr15:93438400-93443200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr15:93438400-93443200	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:93438400-93443200	Weak transcription	Fetal Stomach	stomach
50	chr15:93438400-93443200	Weak transcription	Left Ventricle	heart

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