Variant report

Variant	rs6533780
Chromosome Location	chr4:79487060-79487061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79486780..79488459-chr4:79489706..79491396,2	K562	blood:
2	chr4:79480977..79482887-chr4:79485454..79487082,2	MCF-7	breast:
3	chr4:78783792..78785533-chr4:79484545..79487269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10213249	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650752	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390738	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390739	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496589	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496590	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496591	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496592	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496593	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603462	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975147	0.94[ASW][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672582	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7691521	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696371	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79473600-79487200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
3	chr4:79474600-79488200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:79478800-79489800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:79481800-79521000	Weak transcription	Right Ventricle	heart
6	chr4:79482400-79494800	Weak transcription	Left Ventricle	heart
7	chr4:79482600-79487200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:79482600-79487200	Weak transcription	Placenta	Placenta
9	chr4:79482600-79488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:79482600-79490600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:79482800-79488000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:79482800-79490800	Weak transcription	Fetal Stomach	stomach
13	chr4:79482800-79505000	Weak transcription	Fetal Lung	lung
14	chr4:79483000-79488000	Weak transcription	Pancreas	Pancrea
15	chr4:79483000-79489800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:79483000-79490600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:79483000-79490600	Weak transcription	Aorta	Aorta
18	chr4:79483000-79493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:79483600-79488000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:79484000-79488200	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:79484000-79490000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:79484600-79488000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:79484800-79487200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:79485000-79487200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:79485000-79487400	Enhancers	HUVEC	blood vessel
27	chr4:79485000-79489200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:79485200-79490400	Enhancers	HSMMtube	muscle
29	chr4:79485200-79490600	Enhancers	HSMM	muscle
30	chr4:79485200-79490600	Genic enhancers	NHEK	skin
31	chr4:79485400-79487600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr4:79485600-79490000	Enhancers	NH-A	brain
33	chr4:79485600-79490200	Enhancers	Hela-S3	cervix
34	chr4:79485600-79490600	Enhancers	Stomach Mucosa	stomach
35	chr4:79485800-79487400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr4:79486000-79487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:79486000-79487400	Genic enhancers	Fetal Intestine Small	intestine
38	chr4:79486000-79488200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:79486000-79488800	Enhancers	HMEC	breast
40	chr4:79486200-79491200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr4:79486400-79488400	Enhancers	Lung	lung
42	chr4:79486400-79491200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:79486400-79491400	Enhancers	Fetal Intestine Large	intestine
44	chr4:79486600-79487200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr4:79486600-79488200	Enhancers	NHLF	lung
46	chr4:79486600-79488400	Enhancers	Esophagus	oesophagus
47	chr4:79486600-79488600	Enhancers	Osteobl	bone
48	chr4:79486600-79490000	Enhancers	Right Atrium	heart
49	chr4:79486600-79491000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr4:79486600-79491200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links