Variant report

Variant	rs4239504
Chromosome Location	chr19:40728036-40728037
allele	C/T
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	RAD21	chr19:40727815-40728155	SK-N-SH_RA	brain:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
2	CTCF	chr19:40727839-40728096	NHEK	skin:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
3	CTCF	chr19:40727817-40728186	H1-hESC	embryonic stem cell:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
4	E2F4	chr19:40727913-40728273	GM12878	blood:	n/a	chr19:40728060-40728069
5	FOS	chr19:40727898-40728238	MCF10A-Er-Src	breast:	n/a	chr19:40728030-40728039
6	CTCF	chr19:40727900-40728050	GM12878	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
7	CTCF	chr19:40727920-40728070	NB4	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
8	POU2F2	chr19:40727747-40728254	GM12891	blood:	n/a	chr19:40727983-40727990 chr19:40727981-40727991 chr19:40727979-40727992 chr19:40727982-40727993 chr19:40727982-40727993 chr19:40727979-40727994 chr19:40727982-40727991 chr19:40727982-40727992 chr19:40727980-40727993 chr19:40727981-40727991
9	RAD21	chr19:40727785-40728144	HepG2	liver:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
10	CTCF	chr19:40727750-40728190	K562	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
11	RFX5	chr19:40727757-40728337	GM12878	blood:	n/a	chr19:40728029-40728038
12	EP300	chr19:40727774-40728077	SK-N-SH_RA	brain:	n/a	n/a
13	RAD21	chr19:40727738-40728164	Hela-S3	cervix:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
14	CTCF	chr19:40727851-40728083	GM10266	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
15	CUX1	chr19:40727764-40728182	K562	blood:	n/a	n/a
16	CTCF	chr19:40727743-40728190	A549	lung:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
17	CHD2	chr19:40727830-40728277	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:40727515-40729063	A549	lung:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
19	CTCF	chr19:40727757-40728089	A549	lung:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
20	CTCF	chr19:40727920-40728070	NHEK	skin:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
21	RFX5	chr19:40727622-40728674	IMR90	lung:	n/a	chr19:40728029-40728038
22	YY1	chr19:40727799-40728141	GM12878	blood:	n/a	chr19:40727951-40727961
23	FOS	chr19:40727770-40728277	K562	blood:	n/a	chr19:40727786-40727798 chr19:40728030-40728039
24	POU2F2	chr19:40727723-40728192	GM12878	blood:	n/a	chr19:40727983-40727990 chr19:40727981-40727991 chr19:40727979-40727992 chr19:40727982-40727993 chr19:40727982-40727993 chr19:40727979-40727994 chr19:40727982-40727991 chr19:40727982-40727992 chr19:40727980-40727993 chr19:40727981-40727991
25	POLR2A	chr19:40727873-40728158	HCT-116	colon:	n/a	n/a
26	CTCF	chr19:40727823-40728106	K562	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
27	YY1	chr19:40727801-40728190	GM12878	blood:	n/a	chr19:40727951-40727961
28	YY1	chr19:40727773-40728220	ECC-1	luminal epithelium:	n/a	chr19:40727951-40727961
29	HDAC2	chr19:40727906-40728117	K562	blood:	n/a	n/a
30	CTCF	chr19:40727839-40728087	LNCaP	prostate:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
31	CTCF	chr19:40727860-40728055	H1-hESC	embryonic stem cell:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
32	CTCF	chr19:40727800-40728154	SK-N-SH_RA	brain:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
33	SP2	chr19:40727866-40728270	H1-hESC	embryonic stem cell:	n/a	n/a
34	SP1	chr19:40727843-40728190	K562	blood:	n/a	chr19:40728027-40728048 chr19:40728091-40728112 chr19:40728059-40728080
35	RAD21	chr19:40727751-40728170	GM12878	blood:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
36	FOS	chr19:40727870-40728276	GM12878	blood:	n/a	chr19:40728030-40728039
37	SP1	chr19:40727798-40728255	GM12878	blood:	n/a	chr19:40728027-40728048 chr19:40728091-40728112 chr19:40728059-40728080
38	CTCF	chr19:40727920-40728070	HL-60	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
39	CTCF	chr19:40727861-40728074	GM19239	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
40	SPI1	chr19:40727873-40728123	GM12891	blood:	n/a	n/a
41	POU2F2	chr19:40727668-40728247	GM12878	blood:	n/a	chr19:40727983-40727990 chr19:40727981-40727991 chr19:40727979-40727992 chr19:40727982-40727993 chr19:40727982-40727993 chr19:40727979-40727994 chr19:40727982-40727991 chr19:40727982-40727992 chr19:40727980-40727993 chr19:40727981-40727991
42	CTCF	chr19:40727730-40728115	H1-hESC	embryonic stem cell:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
43	NFIC	chr19:40727819-40728176	HepG2	liver:	n/a	n/a
44	CTCF	chr19:40727742-40728209	MCF-7	breast:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
45	ATF3	chr19:40727668-40728286	A549	lung:	n/a	n/a
46	RAD21	chr19:40727731-40728072	K562	blood:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
47	ELF1	chr19:40727917-40728099	K562	blood:	n/a	chr19:40728007-40728020
48	CTCF	chr19:40727818-40728111	GM19238	blood:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
49	TCF7L2	chr19:40727799-40728210	PANC-1	pancreas:	n/a	n/a
50	YY1	chr19:40727816-40728097	SK-N-SH_RA	brain:	n/a	chr19:40727951-40727961

No.	Distal block	Cell Line	Cell type
1	chr19:40476074..40478265-chr19:40727904..40730547,2	K562	blood:
2	chr19:40645464..40646403-chr19:40727433..40728423,9	K562	blood:
3	chr19:40726603..40728744-chr19:40770942..40773266,2	MCF-7	breast:
4	chr19:40722262..40725312-chr19:40726429..40730380,4	MCF-7	breast:
5	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
6	chr19:40661269..40662213-chr19:40727546..40728443,4	MCF-7	breast:
7	chr19:40728036..40729560-chr19:40729917..40732586,2	K562	blood:

Variant related genes	Relation type
TTC9B	TF binding region
ENSG00000013275	Chromatin interaction
ENSG00000174521	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402740	0.89[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs1129156	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668242	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs11880261	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs12971806	0.80[AMR][1000 genomes]
rs12975651	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs189281	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304189	0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2356229	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs339522	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs339523	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339525	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs339526	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3730050	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs3730051	0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs3746005	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4257318	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs4277441	0.82[ASN][1000 genomes]
rs4337402	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4490099	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4530264	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4558508	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs4802070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802071	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4802073	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4802074	0.85[JPT][hapmap];0.87[MEX][hapmap]
rs4803320	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508936	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7247201	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249146	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs7250897	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs7252471	0.86[CEU][hapmap]
rs7257972	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7258548	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7260249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260517	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs748236	0.80[ASN][1000 genomes]
rs8100018	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8102171	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs8104727	0.82[ASN][1000 genomes]
rs8106744	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110888	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs969531	0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs9749056	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4239504	GRIN2D	cis	cerebellum	SCAN
rs4239504	ZNF221	cis	cerebellum	SCAN
rs4239504	ZNF229	cis	cerebellum	SCAN
rs4239504	IGFL4	cis	parietal	SCAN
rs4239504	SPACA4	cis	cerebellum	SCAN
rs4239504	C19orf47	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40723800-40729000	Weak transcription	Gastric	stomach
3	chr19:40724200-40729000	Weak transcription	Pancreas	Pancrea
4	chr19:40726000-40731600	Weak transcription	NHLF	lung
5	chr19:40726200-40731400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:40726200-40731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:40726200-40731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:40726200-40731600	Weak transcription	NHDF-Ad	bronchial
9	chr19:40726400-40730600	Weak transcription	Hela-S3	cervix
10	chr19:40726400-40731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:40726400-40731600	Weak transcription	A549	lung
12	chr19:40726400-40735200	Weak transcription	K562	blood
13	chr19:40728000-40731600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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