Variant report

Variant	rs248995
Chromosome Location	chr5:79800322-79800323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79793603..79795823-chr5:79798775..79801308,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242706	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10433	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1097307	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1097308	0.84[EUR][1000 genomes]
rs1097309	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs1102116	0.88[EUR][1000 genomes]
rs1103116	0.87[EUR][1000 genomes]
rs1363775	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs168938	0.84[EUR][1000 genomes]
rs168939	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs168940	0.85[CHB][hapmap]
rs171595	0.85[CHB][hapmap]
rs171596	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs171821	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs173597	0.96[EUR][1000 genomes]
rs173599	0.85[CHB][hapmap]
rs174075	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs174076	0.85[CHB][hapmap]
rs1820119	0.87[EUR][1000 genomes]
rs185100	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs187478	0.94[EUR][1000 genomes]
rs187479	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs192313	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2251759	0.82[CHB][hapmap]
rs248999	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs249000	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs249001	0.93[EUR][1000 genomes]
rs249003	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs249006	0.85[CHB][hapmap]
rs249020	0.83[EUR][1000 genomes]
rs249021	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs249023	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs249024	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs249025	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs249026	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs249027	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs249028	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs249029	0.89[EUR][1000 genomes]
rs249030	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs249031	0.89[EUR][1000 genomes]
rs249033	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs249037	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs249038	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs249039	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2544592	0.84[EUR][1000 genomes]
rs2544593	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs2544598	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2544599	0.87[EUR][1000 genomes]
rs2544600	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2544603	0.89[EUR][1000 genomes]
rs2547487	0.84[EUR][1000 genomes]
rs259023	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs259024	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs259025	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs259028	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs259029	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs259030	0.82[CHB][hapmap]
rs259031	0.84[EUR][1000 genomes]
rs259033	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs259034	0.89[EUR][1000 genomes]
rs259037	0.82[CHB][hapmap]
rs259038	0.82[CHB][hapmap]
rs259042	0.85[CHB][hapmap]
rs259043	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs259044	0.85[CHB][hapmap]
rs259045	0.85[CHB][hapmap]
rs259047	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs259048	0.85[CHB][hapmap]
rs259051	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs259052	0.85[CHB][hapmap]
rs259054	0.85[CHB][hapmap]
rs259055	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs2599508	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs3095851	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs394076	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs394170	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs399261	0.88[EUR][1000 genomes]
rs401612	0.89[EUR][1000 genomes]
rs408899	0.88[EUR][1000 genomes]
rs557346	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs701380	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs856765	0.85[CHB][hapmap]
rs863163	0.88[EUR][1000 genomes]
rs969567	0.87[EUR][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	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats 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	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79784800-79806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:79784800-79819400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79785000-79822800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:79785200-79817600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:79790800-79811200	Weak transcription	Placenta	Placenta
6	chr5:79794800-79812800	Weak transcription	Esophagus	oesophagus
7	chr5:79795600-79806000	Weak transcription	Psoas Muscle	Psoas
8	chr5:79798000-79812600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:79798200-79800400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr5:79798200-79811600	Weak transcription	Spleen	Spleen
11	chr5:79799000-79817400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:79799400-79801600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr5:79799600-79801000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr5:79800000-79817000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:79800000-79825600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:79800200-79811400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links