Variant report

Variant	rs249028
Chromosome Location	chr5:79764369-79764370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10052497	0.81[EUR][1000 genomes]
rs10433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10942926	1.00[ASN][1000 genomes]
rs1097307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1097308	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1097309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1102116	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1103116	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13354660	1.00[JPT][hapmap]
rs1363775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423113	0.82[ASN][1000 genomes]
rs168938	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs168939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168940	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs171595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs171596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs171821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs173597	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs174075	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174076	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs1820119	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185100	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187478	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs192313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs194540	0.88[ASN][1000 genomes]
rs194541	0.82[ASN][1000 genomes]
rs2112152	0.86[EUR][1000 genomes]
rs2251759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs248995	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs248999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249001	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249004	0.95[ASN][1000 genomes]
rs249005	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249015	0.91[AFR][1000 genomes]
rs249016	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs249018	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs249019	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs249020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249021	1.00[CEU][hapmap];0.88[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];0.97[ASN][1000 genomes]
rs249023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249027	1.00[CEU][hapmap];1.00[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]
rs249029	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs249031	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249032	0.95[ASN][1000 genomes]
rs249033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs249037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249038	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249040	0.93[AFR][1000 genomes]
rs2544591	0.84[ASN][1000 genomes]
rs2544592	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544598	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544599	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544600	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544603	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544604	1.00[ASN][1000 genomes]
rs2547487	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2547497	0.83[EUR][1000 genomes]
rs259023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs259024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs259025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259026	0.90[ASN][1000 genomes]
rs259027	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs259028	0.86[CHB][hapmap];1.00[ASN][1000 genomes]
rs259029	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259031	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259032	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs259033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259034	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259035	0.83[EUR][1000 genomes]
rs259036	0.82[ASN][1000 genomes]
rs259037	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs259038	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs259039	0.84[ASN][1000 genomes]
rs259040	0.84[ASN][1000 genomes]
rs259041	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259042	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs259043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259044	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259045	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259046	0.84[ASN][1000 genomes]
rs259047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259048	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs259049	1.00[JPT][hapmap]
rs259051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259052	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs259053	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259054	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs259055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2599508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095850	0.88[AFR][1000 genomes]
rs3095851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096111	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs394170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs399261	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401612	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408899	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4704674	1.00[ASN][1000 genomes]
rs557346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6885891	0.82[ASN][1000 genomes]
rs6887302	1.00[JPT][hapmap]
rs701380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs835726	0.87[ASN][1000 genomes]
rs835728	0.83[ASN][1000 genomes]
rs835729	0.92[ASN][1000 genomes]
rs835731	0.82[EUR][1000 genomes]
rs856765	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs856772	0.95[ASN][1000 genomes]
rs863163	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969567	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79722600-79765400	Weak transcription	Fetal Brain Male	brain
2	chr5:79731400-79768000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:79732200-79766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:79733400-79782600	Weak transcription	NHLF	lung
5	chr5:79744800-79783200	Weak transcription	Colonic Mucosa	Colon
6	chr5:79751800-79766400	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:79753000-79765000	Weak transcription	Psoas Muscle	Psoas
8	chr5:79753400-79769600	Weak transcription	HUVEC	blood vessel
9	chr5:79754600-79769600	Weak transcription	Osteobl	bone
10	chr5:79755600-79768000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:79757000-79770000	Weak transcription	NHDF-Ad	bronchial
12	chr5:79757400-79765000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:79757400-79769400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:79758400-79766400	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:79758600-79766200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:79758800-79765000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:79759200-79766000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr5:79759400-79765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:79759400-79765000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:79759400-79765000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:79759400-79765000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:79759400-79765000	Weak transcription	Thymus	Thymus
23	chr5:79759400-79765000	Weak transcription	Spleen	Spleen
24	chr5:79759400-79765200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:79759400-79765800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:79759400-79766000	Weak transcription	Fetal Thymus	thymus
27	chr5:79759400-79766000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:79759400-79766400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:79759400-79767800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:79759400-79768800	Weak transcription	NH-A	brain
31	chr5:79759400-79775000	Weak transcription	Hela-S3	cervix
32	chr5:79759400-79778800	Weak transcription	Small Intestine	intestine
33	chr5:79759400-79779200	Weak transcription	Lung	lung
34	chr5:79759400-79782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:79759600-79765000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:79759600-79766200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:79760200-79765400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:79760200-79766800	Strong transcription	Liver	Liver
39	chr5:79760400-79765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:79760400-79765000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:79760400-79765000	Weak transcription	Right Ventricle	heart
42	chr5:79760400-79765200	Strong transcription	Primary B cells from cord blood	blood
43	chr5:79760400-79765200	Weak transcription	Pancreas	Pancrea
44	chr5:79760400-79766200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:79760800-79765200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:79760800-79765400	Weak transcription	Fetal Heart	heart
47	chr5:79761000-79765000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:79761000-79765400	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr5:79761200-79765000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:79761400-79765200	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links