Variant report

Variant	rs1875884
Chromosome Location	chr15:76638161-76638162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr15:76638133-76639454	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
2	POLR2A	chr15:76637890-76639218	HepG2	liver:	n/a	n/a
3	CTBP2	chr15:76637866-76639885	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr15:76638126-76639093	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:76638078-76639268	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:76638151-76638485	MCF-7	breast:	n/a	n/a
7	MAX	chr15:76637983-76639383	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
8	MAX	chr15:76638058-76638745	MCF-7	breast:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
9	POLR2A	chr15:76638075-76638566	HCT-116	colon:	n/a	n/a
10	MAX	chr15:76638134-76639329	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
11	BACH1	chr15:76637952-76638533	H1-hESC	embryonic stem cell:	n/a	n/a
12	SMARCB1	chr15:76638041-76639719	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr15:76638078-76639374	Hela-S3	cervix:	n/a	n/a
14	HDAC2	chr15:76638031-76638554	HepG2	liver:	n/a	n/a
15	MAX	chr15:76637967-76639337	H1-hESC	embryonic stem cell:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
16	TCF12	chr15:76638071-76638415	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:76638025-76638509	HL-60	blood:	n/a	n/a
18	SUZ12	chr15:76637988-76639646	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr15:76638104-76638604	ECC-1	luminal epithelium:	n/a	n/a
20	NR2F2	chr15:76638034-76638544	MCF-7	breast:	n/a	n/a
21	MAX	chr15:76637994-76639104	ECC-1	luminal epithelium:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
22	E2F6	chr15:76637887-76639835	H1-hESC	embryonic stem cell:	n/a	chr15:76639401-76639411 chr15:76638642-76638652 chr15:76639499-76639509 chr15:76638549-76638561 chr15:76639525-76639535
23	ELF1	chr15:76638134-76638536	HepG2	liver:	n/a	chr15:76638361-76638372
24	E2F6	chr15:76638064-76638824	H1-hESC	embryonic stem cell:	n/a	chr15:76638642-76638652 chr15:76638549-76638561
25	ZBTB7A	chr15:76638028-76639213	ECC-1	luminal epithelium:	n/a	n/a
26	YY1	chr15:76637915-76639211	H1-hESC	embryonic stem cell:	n/a	chr15:76638648-76638659 chr15:76638852-76638863 chr15:76638835-76638844
27	SPI1	chr15:76638132-76638530	HL-60	blood:	n/a	chr15:76638342-76638355 chr15:76638360-76638373
28	SUZ12	chr15:76637608-76640565	NT2-D1	testis:	n/a	n/a
29	POLR2A	chr15:76637947-76638671	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:76638090-76638655	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:76638127-76638214	MCF-7	breast:	n/a	n/a
32	USF2	chr15:76638159-76638461	Hela-S3	cervix:	n/a	chr15:76638226-76638242
33	TCF12	chr15:76637971-76639117	ECC-1	luminal epithelium:	n/a	n/a
34	SMC3	chr15:76637945-76639327	Hela-S3	cervix:	n/a	chr15:76638223-76638233 chr15:76638171-76638179
35	FOXP2	chr15:76637968-76638460	PFSK-1	brain:	n/a	n/a
36	EGR1	chr15:76638088-76638840	H1-hESC	embryonic stem cell:	n/a	chr15:76638331-76638344
37	KAP1	chr15:76637565-76639301	HEK293	kidney:	n/a	n/a
38	RCOR1	chr15:76638152-76639378	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr15:76637726-76639104	HepG2	liver:	n/a	n/a
40	NFIC	chr15:76638092-76638467	HepG2	liver:	n/a	n/a
41	TAF1	chr15:76638085-76638637	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr15:76638143-76638382	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
43	POLR2A	chr15:76638052-76638509	HepG2	liver:	n/a	n/a
44	RAD21	chr15:76637958-76638485	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr15:76637951-76639283	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
46	ZNF143	chr15:76638033-76638776	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr15:76638094-76639167	HepG2	liver:	n/a	n/a
48	MAX	chr15:76638043-76638844	ECC-1	luminal epithelium:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
49	POLR2A	chr15:76637983-76638572	K562	blood:	n/a	n/a
50	HDAC2	chr15:76638098-76638566	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
2	chr15:76625840..76631025-chr15:76637216..76641688,7	MCF-7	breast:
3	chr15:76637265..76640642-chr15:76644223..76647135,3	MCF-7	breast:
4	chr15:76586734..76589503-chr15:76636258..76638931,2	K562	blood:

Variant related genes	Relation type
ENSG00000259514	TF binding region
ENSG00000140386	Chromatin interaction
ENSG00000159556	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072599	0.80[ASN][1000 genomes]
rs12440815	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12441247	0.80[EUR][1000 genomes]
rs12592171	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12592386	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12592420	0.84[ASN][1000 genomes]
rs12593751	0.84[ASN][1000 genomes]
rs12594577	0.80[EUR][1000 genomes]
rs12899871	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902414	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907805	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12914005	0.83[ASN][1000 genomes]
rs12915248	0.83[ASN][1000 genomes]
rs12916573	0.86[ASN][1000 genomes]
rs12917430	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1587381	0.83[ASN][1000 genomes]
rs1588961	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17362383	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363713	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17364076	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17364330	0.83[ASN][1000 genomes]
rs17460201	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17461634	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875885	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117369	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2164101	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs284895	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3866543	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4079681	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4633676	0.82[ASN][1000 genomes]
rs4886799	0.95[ASN][1000 genomes]
rs4886801	0.86[ASN][1000 genomes]
rs56089215	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56216512	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56351018	0.80[EUR][1000 genomes]
rs58684938	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66986092	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67232575	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67263359	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67418609	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67888330	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67920045	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163946	0.83[ASN][1000 genomes]
rs7164060	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7164813	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165025	0.83[ASN][1000 genomes]
rs7179142	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7403276	0.97[ASN][1000 genomes]
rs744336	0.84[AMR][1000 genomes]
rs8025134	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8030411	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8039545	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8043057	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525769	chr15:76632487-76661925	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1875884	SCAPER	cis	Thyroid	GTEx
rs1875884	SCAPER	cis	lung	GTEx
rs1875884	SCAPER	cis	Artery Tibial	GTEx
rs1875884	SCAPER	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76630200-76641800	Weak transcription	A549	lung
2	chr15:76636400-76640200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:76637200-76639000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
4	chr15:76637200-76640000	Weak transcription	K562	blood
5	chr15:76637600-76638600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr15:76637800-76638200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:76637800-76638200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr15:76637800-76638200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr15:76637800-76638200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
10	chr15:76637800-76638200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr15:76637800-76638200	Bivalent Enhancer	Colon Smooth Muscle	Colon
12	chr15:76637800-76638200	Flanking Active TSS	Hela-S3	cervix
13	chr15:76637800-76638600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr15:76637800-76638600	Bivalent Enhancer	Small Intestine	intestine
15	chr15:76637800-76639000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr15:76637800-76640200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:76638000-76638200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
18	chr15:76638000-76638200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:76638000-76638200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:76638000-76638200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr15:76638000-76638200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
22	chr15:76638000-76638200	Bivalent Enhancer	Primary T cells from cord blood	blood
23	chr15:76638000-76638200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:76638000-76638200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:76638000-76638200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:76638000-76638200	Bivalent/Poised TSS	Colonic Mucosa	Colon
27	chr15:76638000-76638200	Bivalent Enhancer	Placenta	Placenta
28	chr15:76638000-76638200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
29	chr15:76638000-76638200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
30	chr15:76638000-76638200	Enhancers	Right Ventricle	heart
31	chr15:76638000-76638200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
33	chr15:76638000-76638400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr15:76638000-76638400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr15:76638000-76638400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr15:76638000-76638400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
38	chr15:76638000-76638400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
39	chr15:76638000-76638400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:76638000-76638400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:76638000-76638400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:76638000-76638400	Bivalent Enhancer	Esophagus	oesophagus
43	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
44	chr15:76638000-76638400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr15:76638000-76638400	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr15:76638000-76638400	Enhancers	Gastric	stomach
47	chr15:76638000-76638400	Bivalent Enhancer	Lung	lung
48	chr15:76638000-76638400	Enhancers	Pancreas	Pancrea
49	chr15:76638000-76638400	Active TSS	Right Atrium	heart
50	chr15:76638000-76638400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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