Variant report

Variant	rs249020
Chromosome Location	chr5:79758501-79758502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10433	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10942926	0.88[ASN][1000 genomes]
rs1097307	0.88[EUR][1000 genomes]
rs1097308	0.88[EUR][1000 genomes]
rs1097309	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1102116	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1103116	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1363775	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs168938	0.88[EUR][1000 genomes]
rs168939	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs171595	0.83[ASN][1000 genomes]
rs171596	0.83[ASN][1000 genomes]
rs171821	0.81[EUR][1000 genomes]
rs173597	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs173599	0.88[ASN][1000 genomes]
rs174075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1820119	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs185100	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187478	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs187479	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs192313	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2112152	0.80[EUR][1000 genomes]
rs2251759	0.88[ASN][1000 genomes]
rs248995	0.83[EUR][1000 genomes]
rs248999	0.83[ASN][1000 genomes]
rs249001	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249003	0.83[ASN][1000 genomes]
rs249004	0.83[ASN][1000 genomes]
rs249005	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249006	0.83[ASN][1000 genomes]
rs249015	0.88[AFR][1000 genomes]
rs249016	0.90[ASN][1000 genomes]
rs249018	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs249019	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs249021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs249023	0.88[ASN][1000 genomes]
rs249024	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249026	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249028	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249029	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249030	0.83[ASN][1000 genomes]
rs249031	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249032	0.83[ASN][1000 genomes]
rs249033	0.88[AFR][1000 genomes]
rs249037	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249038	0.88[ASN][1000 genomes]
rs249039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs249040	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2544592	0.88[EUR][1000 genomes]
rs2544593	0.88[EUR][1000 genomes]
rs2544598	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544599	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544600	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544603	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544604	0.88[ASN][1000 genomes]
rs2547487	0.88[EUR][1000 genomes]
rs259025	0.88[EUR][1000 genomes]
rs259028	0.88[ASN][1000 genomes]
rs259029	0.88[ASN][1000 genomes]
rs259030	0.88[ASN][1000 genomes]
rs259031	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259032	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs259033	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259034	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs259041	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs259043	0.84[EUR][1000 genomes]
rs259055	0.86[EUR][1000 genomes]
rs2599508	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3095850	0.85[AFR][1000 genomes]
rs3095851	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3096111	0.83[EUR][1000 genomes]
rs394076	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs394170	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs399261	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs401612	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs408899	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4704674	0.88[ASN][1000 genomes]
rs557346	0.83[ASN][1000 genomes]
rs701380	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs835729	0.80[ASN][1000 genomes]
rs856765	0.88[ASN][1000 genomes]
rs856772	0.83[ASN][1000 genomes]
rs863163	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs969567	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79704600-79758600	Weak transcription	Gastric	stomach
2	chr5:79722600-79765400	Weak transcription	Fetal Brain Male	brain
3	chr5:79730200-79761400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:79730200-79762200	Weak transcription	Stomach Mucosa	stomach
5	chr5:79730600-79762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:79731400-79768000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:79732200-79758600	Weak transcription	Esophagus	oesophagus
8	chr5:79732200-79766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:79733400-79782600	Weak transcription	NHLF	lung
10	chr5:79735000-79758600	Weak transcription	K562	blood
11	chr5:79736400-79759600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:79738000-79761800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:79738800-79758600	Strong transcription	Liver	Liver
14	chr5:79739800-79760000	Weak transcription	Right Ventricle	heart
15	chr5:79744800-79783200	Weak transcription	Colonic Mucosa	Colon
16	chr5:79748000-79758800	Weak transcription	Hela-S3	cervix
17	chr5:79748000-79760000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:79748400-79758600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:79748800-79758800	Weak transcription	HepG2	liver
20	chr5:79750800-79759000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:79751400-79762000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:79751600-79759400	Strong transcription	Adipose Nuclei	Adipose
23	chr5:79751600-79763600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr5:79751600-79763600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:79751800-79759600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr5:79751800-79761400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:79751800-79761600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:79751800-79766400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:79752800-79758600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:79752800-79758800	Strong transcription	Fetal Intestine Large	intestine
31	chr5:79753000-79765000	Weak transcription	Psoas Muscle	Psoas
32	chr5:79753400-79759200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:79753400-79769600	Weak transcription	HUVEC	blood vessel
34	chr5:79753600-79759200	Weak transcription	HMEC	breast
35	chr5:79754600-79769600	Weak transcription	Osteobl	bone
36	chr5:79755400-79758800	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:79755400-79762200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:79755600-79768000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:79756000-79761200	ZNF genes & repeats	Dnd41	blood
40	chr5:79756400-79760200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:79756400-79761800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:79756800-79758600	Weak transcription	Placenta	Placenta
43	chr5:79756800-79760200	Weak transcription	Fetal Heart	heart
44	chr5:79757000-79758600	Strong transcription	Primary T cells from cord blood	blood
45	chr5:79757000-79758600	Strong transcription	Brain Substantia Nigra	brain
46	chr5:79757000-79759000	Strong transcription	Brain Hippocampus Middle	brain
47	chr5:79757000-79759400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr5:79757000-79760200	Strong transcription	Ovary	ovary
49	chr5:79757000-79760400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:79757000-79761000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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