Variant report

Variant	rs1875883
Chromosome Location	chr15:76638231-76638232
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	chr15:76638182-76638356	GM12878	blood:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
2	MAZ	chr15:76638133-76639454	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
3	POLR2A	chr15:76637890-76639218	HepG2	liver:	n/a	n/a
4	CTBP2	chr15:76637866-76639885	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr15:76638126-76639093	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:76638078-76639268	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:76638215-76638454	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:76638151-76638485	MCF-7	breast:	n/a	n/a
9	MAX	chr15:76637983-76639383	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
10	ELF1	chr15:76638178-76638520	HepG2	liver:	n/a	chr15:76638361-76638372
11	MAX	chr15:76638058-76638745	MCF-7	breast:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
12	POLR2A	chr15:76638075-76638566	HCT-116	colon:	n/a	n/a
13	MAX	chr15:76638134-76639329	Hela-S3	cervix:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
14	BACH1	chr15:76637952-76638533	H1-hESC	embryonic stem cell:	n/a	n/a
15	SMARCB1	chr15:76638041-76639719	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr15:76638078-76639374	Hela-S3	cervix:	n/a	n/a
17	HDAC2	chr15:76638031-76638554	HepG2	liver:	n/a	n/a
18	MAX	chr15:76637967-76639337	H1-hESC	embryonic stem cell:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
19	TCF12	chr15:76638071-76638415	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:76638025-76638509	HL-60	blood:	n/a	n/a
21	SUZ12	chr15:76637988-76639646	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:76638104-76638604	ECC-1	luminal epithelium:	n/a	n/a
23	NR2F2	chr15:76638034-76638544	MCF-7	breast:	n/a	n/a
24	MAX	chr15:76637994-76639104	ECC-1	luminal epithelium:	n/a	chr15:76638331-76638340 chr15:76638340-76638350 chr15:76639091-76639098 chr15:76638879-76638889
25	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
26	ELF1	chr15:76638134-76638536	HepG2	liver:	n/a	chr15:76638361-76638372
27	E2F6	chr15:76638064-76638824	H1-hESC	embryonic stem cell:	n/a	chr15:76638642-76638652 chr15:76638549-76638561
28	ZBTB7A	chr15:76638028-76639213	ECC-1	luminal epithelium:	n/a	n/a
29	YY1	chr15:76637915-76639211	H1-hESC	embryonic stem cell:	n/a	chr15:76638648-76638659 chr15:76638852-76638863 chr15:76638835-76638844
30	SPI1	chr15:76638132-76638530	HL-60	blood:	n/a	chr15:76638342-76638355 chr15:76638360-76638373
31	SUZ12	chr15:76637608-76640565	NT2-D1	testis:	n/a	n/a
32	POLR2A	chr15:76637947-76638671	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr15:76638170-76638362	HepG2	liver:	n/a	n/a
34	POLR2A	chr15:76638178-76638240	Gliobla	brain:	n/a	n/a
35	POLR2A	chr15:76638090-76638655	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr15:76638224-76639363	SK-N-MC	brain:	n/a	n/a
37	USF2	chr15:76638159-76638461	Hela-S3	cervix:	n/a	chr15:76638226-76638242
38	TCF12	chr15:76637971-76639117	ECC-1	luminal epithelium:	n/a	n/a
39	SMC3	chr15:76637945-76639327	Hela-S3	cervix:	n/a	chr15:76638223-76638233 chr15:76638171-76638179
40	FOXP2	chr15:76637968-76638460	PFSK-1	brain:	n/a	n/a
41	EGR1	chr15:76638088-76638840	H1-hESC	embryonic stem cell:	n/a	chr15:76638331-76638344
42	KAP1	chr15:76637565-76639301	HEK293	kidney:	n/a	n/a
43	POLR2A	chr15:76638218-76639173	MCF-7	breast:	n/a	n/a
44	RCOR1	chr15:76638152-76639378	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr15:76637726-76639104	HepG2	liver:	n/a	n/a
46	NFIC	chr15:76638092-76638467	HepG2	liver:	n/a	n/a
47	TAF1	chr15:76638085-76638637	ECC-1	luminal epithelium:	n/a	n/a
48	MYC	chr15:76638143-76638382	HepG2	liver:	n/a	chr15:76638331-76638340 chr15:76638340-76638350
49	POLR2A	chr15:76638052-76638509	HepG2	liver:	n/a	n/a
50	RAD21	chr15:76637958-76638485	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:76638216-76638266	ProgFib	skin:	n/a
2	chr15:76638216-76638266	IMR90	lung:	fetal
3	chr15:76638216-76638266	GM12892	blood:	n/a
4	chr15:76638216-76638266	HMEC	breast:	n/a
5	chr15:76638216-76638266	RPTEC	kidney:	n/a
6	chr15:76638216-76638266	AG04450	lung:	fetal
7	chr15:76638216-76638266	PFSK-1	brain:	n/a
8	chr15:76638216-76638266	GM06990	blood:	n/a
9	chr15:76638216-76638266	HRCEpiC	kidney:	n/a
10	chr15:76638216-76638266	NHBE	bronchial:	n/a
11	chr15:76638216-76638266	HL-60	blood:	n/a
12	chr15:76638216-76638266	HCM	heart:	n/a
13	chr15:76638216-76638266	T-47D	breast:	n/a
14	chr15:76638216-76638266	Hela-S3	cervix:	n/a
15	chr15:76638216-76638266	HPAEpiC	pulmonary alveolar:	n/a
16	chr15:76638216-76638266	SKMC	muscle:	n/a
17	chr15:76638216-76638266	Caco-2	colon:	n/a
18	chr15:76638216-76638266	LNCaP	prostate:	n/a
19	chr15:76638216-76638266	AG09319	gingival:	n/a
20	chr15:76638216-76638266	Jurkat	blood:	n/a
21	chr15:76638216-76638266	GM19239	blood:	n/a
22	chr15:76638216-76638266	HUVEC	blood vessel:	n/a
23	chr15:76638216-76638266	HEK293	kidney:	embryo
24	chr15:76638216-76638266	HRE	kidney:	n/a
25	chr15:76638216-76638266	NH-A	brain:	n/a
26	chr15:76638216-76638266	NT2-D1	testis:	n/a
27	chr15:76638216-76638266	ovcar-3	ovarian:	n/a
28	chr15:76638216-76638266	HCF	heart:	n/a
29	chr15:76638216-76638266	MCF-7	breast:	n/a
30	chr15:76638216-76638266	AG09309	skin:	n/a
31	chr15:76638216-76638266	Hepatocyte	liver:	n/a
32	chr15:76638216-76638266	HAEpiC	amniotic membrane:	n/a
33	chr15:76638216-76638266	NHDF-neo	bronchial:	n/a
34	chr15:76638216-76638266	H1-hESC	embryonic stem cell:	embryo
35	chr15:76638216-76638266	HIPEpiC	eye:	n/a
36	chr15:76638216-76638266	SK-N-SH	brain:	n/a
37	chr15:76638216-76638266	SK-N-SH_RA	brain:	n/a
38	chr15:76638216-76638266	NB4	blood:	n/a
39	chr15:76638216-76638266	BE2_C	brain:	n/a
40	chr15:76638216-76638266	GM12878	blood:	n/a
41	chr15:76638216-76638266	U87	brain:	n/a
42	chr15:76638216-76638266	AG04449	skin:	fetal
43	chr15:76638216-76638266	SAEC	small airway:	n/a
44	chr15:76638216-76638266	SK-N-MC	brain:	n/a
45	chr15:76638216-76638266	CMK	blood:	n/a
46	chr15:76638216-76638266	HCPEpiC	choroid plexus:	n/a
47	chr15:76638216-76638266	HepG2	liver:	n/a
48	chr15:76638216-76638266	A549	lung:	n/a
49	chr15:76638216-76638266	MCF10A-Er-Src	breast:	n/a
50	chr15:76638216-76638266	HNPCEpiC	eye:	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
ENSG00000259514	CpG island
ENSG00000159556	Chromatin interaction
ENSG00000140386	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs157760	0.83[EUR][1000 genomes]
rs157761	0.83[EUR][1000 genomes]
rs157762	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs157775	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs157778	0.83[EUR][1000 genomes]
rs157788	0.83[EUR][1000 genomes]
rs157789	0.83[EUR][1000 genomes]
rs166933	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16968196	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs172244	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs182253	0.83[EUR][1000 genomes]
rs2078437	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460161	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469224	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469535	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469554	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469556	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283796	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs283799	0.83[EUR][1000 genomes]
rs283802	0.83[EUR][1000 genomes]
rs284884	0.81[AMR][1000 genomes]
rs284885	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284893	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284897	0.87[ASN][1000 genomes]
rs284898	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284901	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284902	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284903	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284904	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284905	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284907	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2938695	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2944377	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2948703	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2956873	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2957560	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2957607	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2957611	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2957612	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957613	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs387321	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs454381	0.81[ASN][1000 genomes]
rs4886491	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886492	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494268	0.81[AMR][1000 genomes]
rs8031378	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031672	0.90[EUR][1000 genomes];0.91[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1875883	RP11-685G9.2	cis	Whole Blood	GTEx
rs1875883	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:93 , 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	chr15:76637800-76638600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
7	chr15:76637800-76638600	Bivalent Enhancer	Small Intestine	intestine
8	chr15:76637800-76639000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr15:76637800-76640200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr15:76638000-76638400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr15:76638000-76638400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr15:76638000-76638400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr15:76638000-76638400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr15:76638000-76638400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr15:76638000-76638400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:76638000-76638400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:76638000-76638400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:76638000-76638400	Bivalent Enhancer	Esophagus	oesophagus
21	chr15:76638000-76638400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
22	chr15:76638000-76638400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr15:76638000-76638400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr15:76638000-76638400	Enhancers	Gastric	stomach
25	chr15:76638000-76638400	Bivalent Enhancer	Lung	lung
26	chr15:76638000-76638400	Enhancers	Pancreas	Pancrea
27	chr15:76638000-76638400	Active TSS	Right Atrium	heart
28	chr15:76638000-76638400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
29	chr15:76638000-76638400	Bivalent Enhancer	Stomach Mucosa	stomach
30	chr15:76638000-76638400	Flanking Active TSS	HepG2	liver
31	chr15:76638000-76638400	Bivalent Enhancer	HUVEC	blood vessel
32	chr15:76638000-76638600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr15:76638000-76638600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:76638000-76638600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
35	chr15:76638000-76638800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:76638000-76638800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:76638000-76638800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
38	chr15:76638000-76638800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr15:76638000-76638800	Bivalent Enhancer	NHDF-Ad	bronchial
40	chr15:76638000-76639200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
41	chr15:76638000-76639400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:76638000-76639400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr15:76638000-76639400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
44	chr15:76638000-76639600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
45	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr15:76638000-76639600	Flanking Bivalent TSS/Enh	NHEK	skin
47	chr15:76638000-76639800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:76638000-76639800	Enhancers	Spleen	Spleen
49	chr15:76638000-76640000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr15:76638000-76640000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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