Variant report

Variant	rs12459688
Chromosome Location	chr19:55689403-55689404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55689299-55689587	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:55516495..55518136-chr19:55689009..55691049,2	K562	blood:
2	chr19:55687947..55690269-chr19:55790168..55793036,2	MCF-7	breast:
3	chr19:55688311..55691062-chr19:55894842..55896433,2	MCF-7	breast:
4	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
5	chr19:55688939..55693251-chr19:55917287..55920595,8	K562	blood:
6	chr19:55688567..55692973-chr19:55725028..55730023,9	K562	blood:
7	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
8	chr19:55687645..55690353-chr19:55769334..55772145,4	K562	blood:
9	chr19:55689066..55691659-chr19:55726623..55728296,2	MCF-7	breast:
10	chr19:55688770..55691626-chr19:55917418..55920191,3	K562	blood:
11	chr19:55644998..55647343-chr19:55688157..55689698,2	K562	blood:
12	chr19:55688544..55691824-chr19:55726439..55729589,6	K562	blood:
13	chr19:55626440..55629266-chr19:55687388..55690294,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55689300-55690562	l_1714_chr19:55688749-55693967_brain

No data

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267265	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000129990	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10423713	0.80[ASN][1000 genomes]
rs1128712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459887	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459930	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461148	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461170	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461202	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462211	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463268	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17458	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2071572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278281	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288420	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288518	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2288528	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288529	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745922	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786867	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3803903	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3826887	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848618	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3859544	0.94[ASN][1000 genomes]
rs56666700	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56726774	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58017412	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58218194	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58824375	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59663064	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60176657	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60799292	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61570139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61704307	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247152	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247378	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7248997	0.94[JPT][hapmap]
rs7255625	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8101500	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs890871	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9710458	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55685200-55690400	Weak transcription	Gastric	stomach
2	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
3	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
4	chr19:55685800-55690200	Weak transcription	Osteobl	bone
5	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:55686000-55690200	Weak transcription	A549	lung
8	chr19:55686000-55690200	Weak transcription	NHEK	skin
9	chr19:55686200-55689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:55687000-55689600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:55687200-55689600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:55688000-55690200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:55688200-55689800	Weak transcription	K562	blood
14	chr19:55688600-55689600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:55688600-55689600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:55688600-55690200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:55689200-55689800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:55689200-55691200	Enhancers	Primary hematopoietic stem cells	blood
19	chr19:55689200-55691200	Enhancers	Hela-S3	cervix
20	chr19:55689400-55689600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:55689400-55689600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:55689400-55689600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:55689400-55689600	Bivalent Enhancer	Fetal Brain Male	brain
24	chr19:55689400-55689600	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
25	chr19:55689400-55690000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:55689400-55690000	Enhancers	Dnd41	blood
27	chr19:55689400-55690200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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