Variant report

Variant	rs259038
Chromosome Location	chr5:79696701-79696702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79667050..79669627-chr5:79695393..79697394,2	MCF-7	breast:
2	chr5:79682453..79684405-chr5:79695952..79698525,2	MCF-7	breast:
3	chr5:79695821..79701784-chr5:79701889..79705974,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000039319	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10433	1.00[CHB][hapmap]
rs10474621	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10474629	1.00[CEU][hapmap]
rs10942926	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1097307	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1097308	0.92[ASN][1000 genomes]
rs1097309	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs1103116	0.84[ASN][1000 genomes]
rs1104243	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13354660	0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13359253	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1363775	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs1423113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16877755	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16877757	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168938	0.92[ASN][1000 genomes]
rs168939	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs168940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs171595	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs171596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs171821	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs173599	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs174075	0.82[ASN][1000 genomes]
rs174076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820119	0.82[ASN][1000 genomes]
rs187479	1.00[CHB][hapmap]
rs192313	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs194541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251759	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248995	0.82[CHB][hapmap]
rs248999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs249000	0.85[CHB][hapmap]
rs249003	1.00[CHB][hapmap]
rs249004	0.92[EUR][1000 genomes]
rs249006	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs249016	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs249023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249024	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs249025	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs249026	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs249027	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs249028	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs249032	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs249033	0.86[CHB][hapmap]
rs249037	1.00[CHB][hapmap]
rs249038	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249039	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2544591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2544592	0.92[ASN][1000 genomes]
rs2544593	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs2544598	0.82[ASN][1000 genomes]
rs2544599	0.82[ASN][1000 genomes]
rs2544600	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2544603	0.82[ASN][1000 genomes]
rs2544604	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2547487	0.92[ASN][1000 genomes]
rs259023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259025	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs259026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259027	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259028	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259029	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs259030	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259031	0.82[ASN][1000 genomes]
rs259032	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259033	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs259034	0.82[ASN][1000 genomes]
rs259036	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259039	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259041	0.97[ASN][1000 genomes]
rs259042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259043	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs259044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259046	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259053	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259055	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs2599508	0.86[CHB][hapmap]
rs28496723	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28555465	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3095851	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs3096111	0.87[ASN][1000 genomes]
rs394076	0.86[CHB][hapmap]
rs394170	0.86[CHB][hapmap]
rs401612	0.82[ASN][1000 genomes]
rs4704674	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs557346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6869519	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6885891	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887302	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6898411	1.00[CEU][hapmap]
rs701380	0.86[CHB][hapmap]
rs835726	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs856765	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs856772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs969567	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79693600-79696800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:79694600-79697000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:79695400-79697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:79695400-79702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:79695600-79699200	Weak transcription	HepG2	liver
6	chr5:79695600-79702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:79695600-79702600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:79695600-79702600	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:79695600-79702600	Weak transcription	Osteobl	bone
10	chr5:79695800-79702000	Weak transcription	Brain Anterior Caudate	brain
11	chr5:79695800-79702200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:79695800-79702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:79695800-79702600	Weak transcription	Adipose Nuclei	Adipose
14	chr5:79695800-79702600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:79695800-79702600	Weak transcription	GM12878-XiMat	blood
16	chr5:79696200-79696800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr5:79696200-79697000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:79696200-79702600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:79696400-79697000	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links