Variant report

Variant	rs2304184
Chromosome Location	chr19:40728417-40728418
allele	G/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	CTCF	chr19:40727515-40729063	A549	lung:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
2	RFX5	chr19:40727622-40728674	IMR90	lung:	n/a	chr19:40728029-40728038
3	RFX5	chr19:40727666-40728562	SK-N-SH	brain:	n/a	chr19:40728029-40728038
4	SP1	chr19:40727583-40728518	HCT-116	colon:	n/a	chr19:40728027-40728048 chr19:40728091-40728112 chr19:40728059-40728080
5	CTCF	chr19:40727646-40728492	SK-N-SH	brain:	n/a	chr19:40727956-40727974 chr19:40727962-40727971 chr19:40727959-40727969 chr19:40727951-40727972 chr19:40727957-40727973
6	NFYB	chr19:40727704-40728628	K562	blood:	n/a	chr19:40728057-40728069 chr19:40728090-40728104 chr19:40728087-40728102 chr19:40728058-40728073 chr19:40728028-40728038 chr19:40728058-40728071 chr19:40728090-40728105 chr19:40728089-40728101 chr19:40728058-40728073 chr19:40728055-40728070 chr19:40728023-40728038 chr19:40728090-40728105 chr19:40728058-40728072 chr19:40728026-40728040 chr19:40728026-40728041
7	NFYB	chr19:40727708-40728489	GM12878	blood:	n/a	chr19:40728057-40728069 chr19:40728090-40728104 chr19:40728087-40728102 chr19:40728058-40728073 chr19:40728028-40728038 chr19:40728058-40728071 chr19:40728090-40728105 chr19:40728089-40728101 chr19:40728058-40728073 chr19:40728055-40728070 chr19:40728023-40728038 chr19:40728090-40728105 chr19:40728058-40728072 chr19:40728026-40728040 chr19:40728026-40728041
8	RCOR1	chr19:40727643-40728585	IMR90	lung:	n/a	n/a
9	SP1	chr19:40727605-40728435	HCT-116	colon:	n/a	chr19:40728027-40728048 chr19:40728091-40728112 chr19:40728059-40728080
10	E2F4	chr19:40727808-40728451	MCF10A-Er-Src	breast:	n/a	chr19:40728060-40728069
11	REST	chr19:40725106-40729998	PANC-1	pancreas:	n/a	chr19:40726153-40726161
12	NFYB	chr19:40727694-40728786	Hela-S3	cervix:	n/a	chr19:40728057-40728069 chr19:40728090-40728104 chr19:40728087-40728102 chr19:40728058-40728073 chr19:40728028-40728038 chr19:40728058-40728071 chr19:40728090-40728105 chr19:40728089-40728101 chr19:40728058-40728073 chr19:40728055-40728070 chr19:40728023-40728038 chr19:40728090-40728105 chr19:40728058-40728072 chr19:40728026-40728040 chr19:40728026-40728041
13	RAD21	chr19:40727632-40728634	HCT-116	colon:	n/a	chr19:40727958-40727968 chr19:40727954-40727973
14	RFX5	chr19:40727719-40728548	Hela-S3	cervix:	n/a	chr19:40728029-40728038
15	SMC3	chr19:40727612-40728503	SK-N-SH	brain:	n/a	chr19:40727958-40727972

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
ENSG00000105221	Chromatin interaction
ENSG00000105219	Chromatin interaction
ENSG00000174521	Chromatin interaction
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10402740	0.87[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes]
rs1129156	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668242	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs11880261	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs12971806	0.81[AMR][1000 genomes]
rs12975651	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189281	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304189	0.94[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2356229	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339522	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339523	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs339525	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs339526	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3730050	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs3730051	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs3746005	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4239504	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]
rs4257318	0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs4337402	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4490099	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4530264	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558508	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs4802070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802071	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4802073	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4802074	0.87[MEX][hapmap]
rs4803320	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6508936	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7247201	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249146	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs7250897	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs7252471	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7257972	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7258548	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7260249	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7260517	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs748236	0.81[ASN][1000 genomes]
rs8100018	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8102171	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs8106744	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110888	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs969531	0.84[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap]
rs9749056	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2304184	ZNF221	cis	cerebellum	SCAN
rs2304184	IGFL4	cis	parietal	SCAN
rs2304184	C19orf47	cis	multi-tissue	Pritchard
rs2304184	C19orf47	cis	lymphoblastoid	seeQTL
rs2304184	SPACA4	cis	cerebellum	SCAN
rs2304184	GRIN2D	cis	cerebellum	SCAN
rs2304184	ZNF229	cis	cerebellum	SCAN

Chromatin state (count:17 , 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
14	chr19:40728200-40729000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr19:40728200-40729400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:40728200-40729600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr19:40728200-40729800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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