Variant report

Variant	rs249023
Chromosome Location	chr5:79762214-79762215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79692955..79695721-chr5:79761106..79763084,2	MCF-7	breast:
2	chr5:79762074..79763918-chr5:79765704..79767666,2	MCF-7	breast:
3	chr5:79751639..79754069-chr5:79760868..79763353,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10433	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10474621	0.88[EUR][1000 genomes]
rs10474629	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs10942926	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097307	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs1097308	0.90[ASN][1000 genomes]
rs1097309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1102116	0.95[ASN][1000 genomes]
rs1103116	0.92[ASN][1000 genomes]
rs13354660	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs13359253	0.88[EUR][1000 genomes]
rs1363775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1423113	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16877755	0.88[EUR][1000 genomes]
rs16877757	0.88[EUR][1000 genomes]
rs168938	0.90[ASN][1000 genomes]
rs168939	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs168940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs171595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171821	1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs173597	0.95[ASN][1000 genomes]
rs173599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174075	1.00[ASN][1000 genomes]
rs174076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820119	1.00[ASN][1000 genomes]
rs185100	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs187478	0.95[ASN][1000 genomes]
rs187479	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs192313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs194540	0.88[ASN][1000 genomes]
rs194541	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2251759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248995	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs248999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs249001	0.95[ASN][1000 genomes]
rs249003	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs249004	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249005	0.95[ASN][1000 genomes]
rs249006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249016	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs249020	0.88[ASN][1000 genomes]
rs249021	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs249024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249025	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249026	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249027	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs249029	0.95[ASN][1000 genomes]
rs249030	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249031	0.95[ASN][1000 genomes]
rs249032	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs249033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs249037	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs249038	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249039	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[ASN][1000 genomes]
rs2544591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2544592	0.90[ASN][1000 genomes]
rs2544593	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2544598	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2544599	1.00[ASN][1000 genomes]
rs2544600	0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs2544603	1.00[ASN][1000 genomes]
rs2544604	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2547487	0.90[ASN][1000 genomes]
rs259023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.90[ASN][1000 genomes]
rs259026	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259027	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs259028	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259029	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs259030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259031	1.00[ASN][1000 genomes]
rs259032	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259033	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[ASN][1000 genomes]
rs259034	1.00[ASN][1000 genomes]
rs259036	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs259039	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs259040	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259041	0.84[ASN][1000 genomes]
rs259042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259043	1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs259044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259046	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259049	1.00[JPT][hapmap]
rs259051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs259053	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs259055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2599508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28496723	0.88[EUR][1000 genomes]
rs28555465	0.88[EUR][1000 genomes]
rs3095851	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3096111	0.85[ASN][1000 genomes]
rs394076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs394170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs399261	0.95[ASN][1000 genomes]
rs401612	1.00[ASN][1000 genomes]
rs408899	0.95[ASN][1000 genomes]
rs4704674	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6869519	0.88[EUR][1000 genomes]
rs6885891	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6887302	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6898411	1.00[CEU][hapmap]
rs701380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs835726	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs835728	0.83[ASN][1000 genomes]
rs835729	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs856765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856772	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs863163	0.95[ASN][1000 genomes]
rs969567	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:117 , 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	chr5:79751600-79763600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr5:79751600-79763600	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:79751800-79766400	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:79753000-79765000	Weak transcription	Psoas Muscle	Psoas
10	chr5:79753400-79769600	Weak transcription	HUVEC	blood vessel
11	chr5:79754600-79769600	Weak transcription	Osteobl	bone
12	chr5:79755600-79768000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:79757000-79770000	Weak transcription	NHDF-Ad	bronchial
14	chr5:79757200-79763400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr5:79757400-79762800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:79757400-79765000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:79757400-79769400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:79758400-79766400	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:79758600-79763400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr5:79758600-79766200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:79758800-79762800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:79758800-79765000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:79759200-79766000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr5:79759400-79762400	Weak transcription	HSMM	muscle
25	chr5:79759400-79762600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:79759400-79762800	Weak transcription	Gastric	stomach
27	chr5:79759400-79764000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:79759400-79765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:79759400-79765000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:79759400-79765000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:79759400-79765000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:79759400-79765000	Weak transcription	Thymus	Thymus
33	chr5:79759400-79765000	Weak transcription	Spleen	Spleen
34	chr5:79759400-79765200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:79759400-79765800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:79759400-79766000	Weak transcription	Fetal Thymus	thymus
37	chr5:79759400-79766000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:79759400-79766400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:79759400-79767800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:79759400-79768800	Weak transcription	NH-A	brain
41	chr5:79759400-79775000	Weak transcription	Hela-S3	cervix
42	chr5:79759400-79778800	Weak transcription	Small Intestine	intestine
43	chr5:79759400-79779200	Weak transcription	Lung	lung
44	chr5:79759400-79782800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:79759600-79765000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:79759600-79766200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:79760000-79762400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:79760000-79763200	Strong transcription	Fetal Stomach	stomach
49	chr5:79760200-79762400	Strong transcription	Adipose Nuclei	Adipose
50	chr5:79760200-79762600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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