Variant report

Variant	rs234365
Chromosome Location	chr19:40475211-40475212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr19:40475059-40475659	MCF10A-Er-Src	breast:	n/a	n/a
2	NR3C1	chr19:40475052-40475563	A549	lung:	n/a	n/a
3	POLR2A	chr19:40475166-40475858	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:40472172-40495393	PANC-1	pancreas:	n/a	n/a
5	FOS	chr19:40475038-40475453	MCF10A-Er-Src	breast:	n/a	n/a
6	FOXA1	chr19:40475095-40475403	A549	lung:	n/a	n/a
7	TBP	chr19:40475147-40475460	HepG2	liver:	n/a	n/a
8	FOS	chr19:40475149-40475408	MCF10A-Er-Src	breast:	n/a	n/a
9	SIN3AK20	chr19:40473718-40478635	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40324934..40327706-chr19:40474760..40476442,2	K562	blood:
2	chr19:40472468..40476413-chr19:40479730..40482224,3	MCF-7	breast:
3	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:
4	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
5	chr19:40473843..40476809-chr19:40580140..40582711,2	K562	blood:
6	chr19:40474771..40476679-chr19:40510895..40512826,2	K562	blood:
7	chr19:40474771..40476909-chr19:40510895..40513738,3	K562	blood:
8	chr19:40475179..40477026-chr19:40560831..40562342,2	K562	blood:
9	chr19:40461619..40464271-chr19:40474236..40476089,2	K562	blood:
10	chr19:40473089..40482317-chr19:40483091..40492558,21	K562	blood:

No data

Variant related genes	Relation type
PSMC4	TF binding region
ENSG00000013275	Chromatin interaction
ENSG00000128000	Chromatin interaction
ENSG00000187187	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs170900	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2231738	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs234340	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2355720	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs337780	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs337782	0.86[EUR][1000 genomes]
rs3754	0.95[ASN][1000 genomes]
rs3760919	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3760923	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3786938	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3826919	0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs424365	0.83[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427461	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs55798334	0.82[EUR][1000 genomes]
rs59030876	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7249286	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7249890	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8106269	0.83[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs8109718	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs8109879	0.82[ASN][1000 genomes]
rs9749001	0.86[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	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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 miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:40460800-40476000	Weak transcription	Psoas Muscle	Psoas
3	chr19:40461600-40475400	Weak transcription	Brain Substantia Nigra	brain
4	chr19:40466200-40476200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:40468600-40475600	Weak transcription	Brain Anterior Caudate	brain
6	chr19:40472600-40475400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:40472600-40475600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:40472800-40476000	Weak transcription	Brain Angular Gyrus	brain
9	chr19:40473000-40476000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr19:40473000-40476000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:40473400-40475400	Enhancers	Primary T cells from cord blood	blood
12	chr19:40474000-40476200	Weak transcription	Fetal Kidney	kidney
13	chr19:40474000-40476200	Enhancers	HepG2	liver
14	chr19:40474200-40475600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:40474200-40476200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:40474400-40476000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr19:40474600-40476000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:40474800-40475600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr19:40474800-40475600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:40474800-40476200	Enhancers	Primary B cells from cord blood	blood
21	chr19:40474800-40476200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr19:40474800-40476200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:40474800-40476200	Enhancers	Esophagus	oesophagus
24	chr19:40474800-40476200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr19:40475000-40475600	Enhancers	K562	blood
26	chr19:40475000-40476000	Enhancers	HMEC	breast
27	chr19:40475000-40476200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:40475000-40476200	Weak transcription	Colonic Mucosa	Colon
29	chr19:40475000-40476400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr19:40475200-40475400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:40475200-40475400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr19:40475200-40475400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:40475200-40475400	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr19:40475200-40475400	Enhancers	Right Ventricle	heart
35	chr19:40475200-40475400	Enhancers	Hela-S3	cervix
36	chr19:40475200-40475600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:40475200-40475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:40475200-40475800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:40475200-40475800	Enhancers	A549	lung
40	chr19:40475200-40475800	Flanking Active TSS	GM12878-XiMat	blood
41	chr19:40475200-40475800	Flanking Active TSS	NHEK	skin
42	chr19:40475200-40476000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:40475200-40476000	Enhancers	Brain Hippocampus Middle	brain
44	chr19:40475200-40476200	Enhancers	Primary B cells from peripheral blood	blood
45	chr19:40475200-40476200	Enhancers	Adipose Nuclei	Adipose
46	chr19:40475200-40476200	Enhancers	Fetal Thymus	thymus
47	chr19:40475200-40476200	Enhancers	Stomach Mucosa	stomach
48	chr19:40475200-40476600	Flanking Active TSS	Dnd41	blood

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