Variant report

Variant	rs4490099
Chromosome Location	chr19:40731491-40731492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr19:40731408-40731644	K562	blood:	n/a	n/a
2	SIN3AK20	chr19:40731136-40743299	PANC-1	pancreas:	n/a	n/a
3	RCOR1	chr19:40731399-40731828	HepG2	liver:	n/a	n/a
4	MAX	chr19:40730018-40731567	HCT-116	colon:	n/a	n/a
5	ELF1	chr19:40731366-40731721	K562	blood:	n/a	chr19:40731534-40731547
6	MAX	chr19:40731436-40733060	HepG2	liver:	n/a	chr19:40732929-40732939
7	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
8	REST	chr19:40731178-40733034	PANC-1	pancreas:	n/a	chr19:40732699-40732708 chr19:40732184-40732197
9	POLR2A	chr19:40731437-40731704	HCT-116	colon:	n/a	n/a
10	POLR2A	chr19:40731289-40733027	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40730457..40732107-chr19:40746793..40748406,2	MCF-7	breast:
2	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:
3	chr19:40728036..40729560-chr19:40729917..40732586,2	K562	blood:
4	chr19:40730680..40732953-chr19:40742312..40745155,2	K562	blood:
5	chr19:40723230..40725206-chr19:40730553..40733160,2	MCF-7	breast:
6	chr19:40730135..40732831-chr19:40769478..40772203,2	MCF-7	breast:
7	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
8	chr19:40731324..40733318-chr19:40786434..40789035,2	MCF-7	breast:

No data

Variant related genes	Relation type
CNTD2	TF binding region
ENSG00000105219	Chromatin interaction
ENSG00000207631	Chromatin interaction
ENSG00000174521	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.94[MEX][hapmap]
rs1129156	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];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11668242	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs11880261	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12975651	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304184	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]
rs2304189	0.94[CHB][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356229	0.80[ASN][1000 genomes]
rs339522	0.80[ASN][1000 genomes]
rs339525	0.80[ASN][1000 genomes]
rs339526	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs3730050	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3730051	0.90[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3746005	0.81[EUR][1000 genomes]
rs4239504	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]
rs4239506	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4257318	0.81[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4277441	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4332845	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4337402	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4499338	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4530264	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4558508	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802070	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802071	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802073	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4802074	0.90[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4803320	0.90[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508936	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7247201	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7249146	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs7250897	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7257972	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7258548	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7260249	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7260517	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs748236	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8100018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8102171	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104727	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8106744	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110888	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs969531	0.90[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9749056	0.80[ASN][1000 genomes]
rs9749283	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4490099	SPACA4	cis	cerebellum	SCAN
rs4490099	TMEM91	cis	parietal	SCAN
rs4490099	ERCC1	cis	parietal	SCAN
rs4490099	ZNF221	cis	cerebellum	SCAN
rs4490099	IGFL4	cis	parietal	SCAN
rs4490099	SYMPK	cis	cerebellum	SCAN
rs4490099	ZNF221	cis	parietal	SCAN
rs4490099	C19orf47	cis	lymphoblastoid	seeQTL
rs4490099	APOE	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40726000-40731600	Weak transcription	NHLF	lung
3	chr19:40726200-40731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:40726200-40731600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:40726200-40731600	Weak transcription	NHDF-Ad	bronchial
6	chr19:40726400-40731600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:40726400-40731600	Weak transcription	A549	lung
8	chr19:40726400-40735200	Weak transcription	K562	blood
9	chr19:40728000-40731600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:40729400-40732000	Weak transcription	Gastric	stomach
11	chr19:40729600-40731600	Weak transcription	Lung	lung
12	chr19:40729600-40732000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:40730600-40732000	Enhancers	Hela-S3	cervix
14	chr19:40730800-40731800	Enhancers	Liver	Liver
15	chr19:40730800-40732000	Weak transcription	Right Ventricle	heart
16	chr19:40731200-40731600	Weak transcription	Placenta	Placenta
17	chr19:40731400-40731600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:40731400-40731600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
19	chr19:40731400-40731600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:40731400-40731600	Enhancers	Adipose Nuclei	Adipose
21	chr19:40731400-40731600	Bivalent Enhancer	Brain Hippocampus Middle	brain
22	chr19:40731400-40731600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
23	chr19:40731400-40731600	Bivalent Enhancer	Esophagus	oesophagus
24	chr19:40731400-40731600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr19:40731400-40731600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr19:40731400-40731600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
27	chr19:40731400-40731800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
28	chr19:40731400-40731800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr19:40731400-40731800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:40731400-40731800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
31	chr19:40731400-40731800	Bivalent/Poised TSS	Fetal Lung	lung
32	chr19:40731400-40732000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr19:40731400-40732000	Bivalent Enhancer	Fetal Intestine Small	intestine
34	chr19:40731400-40732000	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr19:40731400-40732000	Flanking Bivalent TSS/Enh	HepG2	liver
36	chr19:40731400-40732000	Bivalent Enhancer	NHEK	skin
37	chr19:40731400-40732400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
38	chr19:40731400-40732600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:40731400-40732800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr19:40731400-40732800	Enhancers	Spleen	Spleen
41	chr19:40731400-40733000	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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