Variant report

Variant	rs4808802
Chromosome Location	chr19:18577873-18577874
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18575464..18579063-chr19:18579227..18581262,3	MCF-7	breast:
2	chr19:18568659..18571557-chr19:18575200..18577928,3	K562	blood:
3	chr19:18577412..18579781-chr19:18615070..18616798,2	K562	blood:
4	chr19:18575653..18580587-chr19:18588169..18591423,6	K562	blood:
5	chr19:18527968..18530856-chr19:18575809..18578899,3	MCF-7	breast:
6	chr19:18575799..18578252-chr19:18699046..18700945,3	MCF-7	breast:
7	chr19:18576760..18579549-chr19:18629981..18632725,2	K562	blood:
8	chr19:18577781..18580472-chr19:18624085..18625871,2	MCF-7	breast:
9	chr19:18577693..18579914-chr19:18698517..18700707,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130511	Chromatin interaction
ENSG00000006015	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10164323	0.86[JPT][hapmap]
rs10402322	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409346	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10409408	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410797	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10413922	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10416993	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418331	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418554	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10420384	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10426768	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045631	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11086110	0.81[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs11668704	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670392	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672385	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879757	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980726	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982295	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12983263	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469412	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469413	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971093	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013069	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2162797	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303692	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28534973	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2891676	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213500	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35004712	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35742476	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4006662	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4303657	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580317	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808135	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808803	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808805	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808807	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808808	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808811	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808812	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808813	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55715336	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57923655	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6512268	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6512269	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512270	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6512271	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7246788	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247540	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249760	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251640	1.00[CHB][hapmap]
rs7252130	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7252185	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255936	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256530	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258891	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7259135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7507218	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8100343	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102717	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104247	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106068	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8106332	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111397	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111582	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111824	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8112372	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112859	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888668	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs888669	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
2	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
6	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
7	nsv1060687	chr19:18522527-18643218	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4808802	SSBP4	Cis_1M	lymphoblastoid	RTeQTL
rs4808802	LOC646044///SSBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18553400-18579000	Weak transcription	Fetal Kidney	kidney
2	chr19:18553800-18578000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:18562200-18580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:18562200-18580600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:18562800-18580800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:18567800-18578200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:18568200-18583800	Weak transcription	Fetal Brain Male	brain
8	chr19:18571400-18584200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:18571800-18581200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:18571800-18589600	Weak transcription	HUVEC	blood vessel
11	chr19:18572200-18581000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:18572200-18589600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:18572400-18581200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:18572400-18583200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:18572600-18580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:18572600-18581000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:18572600-18581200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:18572600-18592400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:18572800-18578000	Weak transcription	HSMM	muscle
20	chr19:18574800-18578200	Enhancers	Brain Hippocampus Middle	brain
21	chr19:18574800-18578400	Enhancers	Left Ventricle	heart
22	chr19:18575000-18578200	Genic enhancers	Fetal Stomach	stomach
23	chr19:18575000-18578400	Enhancers	Adipose Nuclei	Adipose
24	chr19:18575000-18578400	Enhancers	Brain Substantia Nigra	brain
25	chr19:18575000-18579000	Enhancers	Right Atrium	heart
26	chr19:18575000-18582000	Enhancers	Liver	Liver
27	chr19:18575200-18578200	Enhancers	Brain Angular Gyrus	brain
28	chr19:18575200-18578400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:18575200-18578400	Enhancers	Ovary	ovary
30	chr19:18575200-18580000	Genic enhancers	Esophagus	oesophagus
31	chr19:18575200-18581400	Enhancers	Psoas Muscle	Psoas
32	chr19:18575200-18581600	Enhancers	Stomach Mucosa	stomach
33	chr19:18575400-18578200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr19:18575400-18579000	Weak transcription	HSMMtube	muscle
35	chr19:18575400-18607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:18575600-18587000	Weak transcription	Primary B cells from cord blood	blood
37	chr19:18575800-18578000	Genic enhancers	Right Ventricle	heart
38	chr19:18575800-18585000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:18575800-18590800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:18576000-18578000	Genic enhancers	NHLF	lung
41	chr19:18576000-18581000	Weak transcription	K562	blood
42	chr19:18576000-18584000	Weak transcription	Small Intestine	intestine
43	chr19:18576200-18578000	Enhancers	Colon Smooth Muscle	Colon
44	chr19:18576200-18578000	Weak transcription	NH-A	brain
45	chr19:18576200-18578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:18576200-18580600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:18576200-18590800	Weak transcription	Aorta	Aorta
48	chr19:18576400-18578000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:18576400-18578000	Weak transcription	HMEC	breast
50	chr19:18576400-18578000	Weak transcription	Osteobl	bone

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