Variant report

Variant	rs259053
Chromosome Location	chr5:79704614-79704615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79704445..79706088-chr5:79748731..79750279,2	K562	blood:
2	chr5:79704434..79706120-chr5:79706146..79708385,2	K562	blood:
3	chr16:31492241..31494807-chr5:79702904..79705274,2	MCF-7	breast:
4	chr5:79702114..79706204-chr5:79947823..79953616,8	MCF-7	breast:
5	chr5:79704087..79706169-chr5:79706671..79709625,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140675	Chromatin interaction
ENSG00000113318	Chromatin interaction
ENSG00000039319	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10433	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10474621	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10474629	1.00[CEU][hapmap]
rs10942926	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1097307	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1097308	0.95[ASN][1000 genomes]
rs1097309	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1103116	0.87[ASN][1000 genomes]
rs1104243	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13354660	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13359253	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1363775	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1423113	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16877755	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16877757	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs168938	0.95[ASN][1000 genomes]
rs168939	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs168940	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs171596	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs171821	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs173599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs174075	0.84[ASN][1000 genomes]
rs174076	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820119	0.84[ASN][1000 genomes]
rs185100	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs187479	0.86[CHB][hapmap]
rs192313	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs194541	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248999	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs249000	1.00[JPT][hapmap]
rs249003	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs249004	0.92[EUR][1000 genomes]
rs249006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs249016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs249021	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs249023	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs249024	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs249025	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs249026	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs249027	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs249028	1.00[JPT][hapmap];0.84[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	1.00[JPT][hapmap]
rs249037	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs249038	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs249039	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544591	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544592	0.95[ASN][1000 genomes]
rs2544593	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2544598	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544599	0.84[ASN][1000 genomes]
rs2544600	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544603	0.84[ASN][1000 genomes]
rs2544604	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547487	0.95[ASN][1000 genomes]
rs259023	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259024	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259025	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs259026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259027	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259028	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259029	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs259030	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259031	0.84[ASN][1000 genomes]
rs259032	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259033	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259034	0.84[ASN][1000 genomes]
rs259036	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259037	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]
rs259038	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]
rs259039	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259040	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259041	1.00[ASN][1000 genomes]
rs259042	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259043	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259044	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259045	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259046	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259047	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259048	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259049	1.00[JPT][hapmap]
rs259051	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][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]
rs259052	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259054	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259055	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2599508	1.00[JPT][hapmap]
rs28496723	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28555465	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095851	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3096111	0.90[ASN][1000 genomes]
rs394076	1.00[JPT][hapmap]
rs394170	1.00[JPT][hapmap]
rs401612	0.84[ASN][1000 genomes]
rs4704674	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs557346	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6869519	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6885891	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6887302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6898411	1.00[CEU][hapmap]
rs701380	1.00[JPT][hapmap]
rs835726	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs835729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs856765	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs856772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs969567	0.84[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79702600-79705400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:79702600-79705400	Active TSS	Brain Anterior Caudate	brain
3	chr5:79702600-79705400	Active TSS	HSMMtube	muscle
4	chr5:79702600-79706000	Active TSS	Fetal Kidney	kidney
5	chr5:79702600-79706000	Active TSS	NHLF	lung
6	chr5:79702800-79704800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:79702800-79704800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:79702800-79704800	Active TSS	Thymus	Thymus
9	chr5:79702800-79705000	Active TSS	Fetal Intestine Large	intestine
10	chr5:79702800-79705200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr5:79702800-79705400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:79702800-79705400	Active TSS	Brain Cingulate Gyrus	brain
13	chr5:79702800-79705400	Active TSS	Hela-S3	cervix
14	chr5:79702800-79705400	Active TSS	HSMM	muscle
15	chr5:79702800-79705600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:79702800-79705600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:79702800-79705600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:79702800-79705800	Active TSS	Brain Angular Gyrus	brain
19	chr5:79702800-79705800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr5:79702800-79705800	Active TSS	Fetal Stomach	stomach
21	chr5:79702800-79706000	Active TSS	Psoas Muscle	Psoas
22	chr5:79702800-79706000	Active TSS	Right Ventricle	heart
23	chr5:79702800-79706200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:79702800-79706200	Active TSS	Ovary	ovary
25	chr5:79702800-79706400	Active TSS	Right Atrium	heart
26	chr5:79702800-79706800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:79703000-79704800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:79703000-79704800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr5:79703000-79704800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:79703000-79704800	Active TSS	Aorta	Aorta
31	chr5:79703000-79704800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr5:79703000-79704800	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr5:79703000-79704800	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr5:79703000-79705000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr5:79703000-79705000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr5:79703000-79705000	Active TSS	Rectal Smooth Muscle	rectum
37	chr5:79703000-79705000	Active TSS	NHEK	skin
38	chr5:79703000-79705400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr5:79703000-79705400	Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:79703000-79705400	Active TSS	Brain Substantia Nigra	brain
41	chr5:79703000-79705600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr5:79703000-79705600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:79703000-79705600	Active TSS	Stomach Smooth Muscle	stomach
44	chr5:79703000-79706000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr5:79703000-79706000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:79703000-79706000	Active TSS	Fetal Brain Female	brain
47	chr5:79703000-79706000	Active TSS	Fetal Lung	lung
48	chr5:79703000-79706200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:79703000-79706200	Active TSS	NHDF-Ad	bronchial
50	chr5:79703000-79706400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links