Variant report

Variant	rs11878238
Chromosome Location	chr19:55688280-55688281
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr19:55688110-55688381	K562	blood:	n/a	n/a
2	POLR2A	chr19:55688082-55688757	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:55685402-55688569	H1-neurons	neurons:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:55687947..55690269-chr19:55790168..55793036,2	MCF-7	breast:
2	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
3	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
4	chr19:55687645..55690353-chr19:55769334..55772145,4	K562	blood:
5	chr19:55644998..55647343-chr19:55688157..55689698,2	K562	blood:
6	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
7	chr19:55687032..55688994-chr19:55895402..55898104,2	K562	blood:
8	chr19:55626440..55629266-chr19:55687388..55690294,2	K562	blood:

No data

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000133265	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000125503	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10412231	0.95[AFR][1000 genomes]
rs10416615	0.85[AFR][1000 genomes]
rs11880446	0.85[AFR][1000 genomes]
rs12104357	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2288524	1.00[EUR][1000 genomes]
rs28668417	0.90[AFR][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:23 , 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	chr19:55686000-55689200	Weak transcription	Hela-S3	cervix
7	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:55686000-55690200	Weak transcription	A549	lung
9	chr19:55686000-55690200	Weak transcription	NHEK	skin
10	chr19:55686200-55689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:55687000-55689600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:55687200-55689000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:55687200-55689600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:55687400-55689400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:55687600-55688400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr19:55687600-55689400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:55687800-55688600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr19:55688000-55688600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:55688000-55689200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:55688000-55690200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:55688200-55688400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
22	chr19:55688200-55688600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:55688200-55689800	Weak transcription	K562	blood

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