Variant report

Variant	rs28668475
Chromosome Location	chr19:51844246-51844247
allele	C/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	MAZ	chr19:51841761-51844263	K562	blood:	n/a	chr19:51843203-51843213 chr19:51842127-51842137 chr19:51841906-51841913 chr19:51843926-51843936
2	POLR2A	chr19:51844207-51844626	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:51841814-51851408	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:51842878-51844694	A549	lung:	n/a	n/a
5	POLR2A	chr19:51844107-51844692	A549	lung:	n/a	n/a
6	POLR2A	chr19:51843153-51844477	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:51841748-51844486	K562	blood:	n/a	n/a
8	CTCF	chr19:51841495-51844609	A549	lung:	n/a	chr19:51843444-51843457 chr19:51842691-51842712 chr19:51842697-51842713 chr19:51843837-51843850
9	POLR2A	chr19:51842902-51844631	K562	blood:	n/a	n/a
10	POLR2A	chr19:51842928-51844501	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
2	chr19:51843178..51845619-chr19:52074404..52075904,2	K562	blood:
3	chr19:51841314..51846809-chr19:51868154..51872523,19	K562	blood:
4	chr19:51841175..51847735-chr19:51867771..51872496,21	MCF-7	breast:
5	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
6	chr19:51841590..51847683-chr19:51867906..51872035,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267984	TF binding region
VSIG10L	TF binding region
ENSG00000262874	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000269403	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1035454	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10414211	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419062	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10424579	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084068	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11878664	0.99[ASN][1000 genomes]
rs12463376	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2011612	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34380065	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259266	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105710	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	esv3380303	chr19:51842165-51844913	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51842000-51845200	Active TSS	Esophagus	oesophagus
2	chr19:51842600-51844600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:51842800-51847200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:51843000-51844800	Active TSS	HepG2	liver
5	chr19:51843000-51847400	Weak transcription	Dnd41	blood
6	chr19:51843000-51852200	Weak transcription	Fetal Heart	heart
7	chr19:51843000-51857600	Weak transcription	Fetal Kidney	kidney
8	chr19:51843200-51857400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:51843400-51844400	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr19:51843400-51844800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:51843600-51844400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:51843600-51844400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:51843600-51844400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:51843600-51848000	Weak transcription	Primary T cells from cord blood	blood
15	chr19:51843600-51854000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:51843800-51844400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:51843800-51844400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:51843800-51844400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:51843800-51844400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr19:51843800-51844400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:51843800-51844400	Bivalent Enhancer	Fetal Intestine Large	intestine
22	chr19:51843800-51844400	Bivalent Enhancer	Fetal Intestine Small	intestine
23	chr19:51843800-51847400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:51843800-51848000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr19:51843800-51848000	Weak transcription	Lung	lung
26	chr19:51843800-51848600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:51843800-51848800	Enhancers	Primary B cells from peripheral blood	blood
28	chr19:51843800-51849600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:51843800-51854400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:51843800-51857600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr19:51844000-51844400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:51844000-51844400	Enhancers	Adipose Nuclei	Adipose
33	chr19:51844000-51844400	Flanking Active TSS	A549	lung
34	chr19:51844000-51844600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:51844000-51844600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:51844000-51844600	Bivalent Enhancer	Placenta	Placenta
37	chr19:51844000-51845000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:51844000-51847200	Weak transcription	Primary B cells from cord blood	blood
39	chr19:51844000-51847200	Weak transcription	GM12878-XiMat	blood
40	chr19:51844000-51847400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:51844000-51847400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:51844000-51847400	Weak transcription	Left Ventricle	heart
43	chr19:51844000-51847600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:51844000-51848000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:51844000-51848000	Weak transcription	Brain Anterior Caudate	brain
46	chr19:51844000-51848000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:51844000-51848000	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:51844000-51848000	Weak transcription	Gastric	stomach
49	chr19:51844000-51848000	Weak transcription	Ovary	ovary
50	chr19:51844000-51848000	Weak transcription	Pancreas	Pancrea

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