Variant report

Variant	rs3776976
Chromosome Location	chr5:80111665-80111666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11950254	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11956599	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12515222	0.85[EUR][1000 genomes]
rs12515548	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518711	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12521191	0.85[EUR][1000 genomes]
rs12521371	0.82[EUR][1000 genomes]
rs12521389	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521539	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522132	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522866	0.84[EUR][1000 genomes]
rs13154537	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13165877	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13168327	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13178429	0.81[EUR][1000 genomes]
rs13178892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13179210	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13186354	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1679115	0.96[ASN][1000 genomes]
rs168653	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2112415	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306371	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245340	0.90[ASN][1000 genomes]
rs245341	0.91[ASN][1000 genomes]
rs245348	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs245355	0.95[ASN][1000 genomes]
rs245356	0.95[ASN][1000 genomes]
rs245357	0.95[ASN][1000 genomes]
rs245360	0.95[ASN][1000 genomes]
rs245364	0.85[ASN][1000 genomes]
rs245372	0.89[ASN][1000 genomes]
rs245373	0.93[ASN][1000 genomes]
rs245374	0.95[ASN][1000 genomes]
rs245379	0.93[ASN][1000 genomes]
rs245380	0.90[ASN][1000 genomes]
rs245385	0.95[ASN][1000 genomes]
rs245386	0.93[ASN][1000 genomes]
rs245389	0.92[ASN][1000 genomes]
rs26278	0.96[ASN][1000 genomes]
rs26279	0.89[ASN][1000 genomes]
rs27366	0.94[ASN][1000 genomes]
rs27494	0.89[ASN][1000 genomes]
rs27887	0.89[ASN][1000 genomes]
rs2897298	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs32963	0.89[ASN][1000 genomes]
rs32964	0.89[ASN][1000 genomes]
rs32967	0.89[ASN][1000 genomes]
rs32968	0.89[ASN][1000 genomes]
rs32988	0.98[ASN][1000 genomes]
rs32989	0.98[ASN][1000 genomes]
rs32995	0.86[ASN][1000 genomes]
rs32999	0.98[ASN][1000 genomes]
rs34205517	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34274010	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34560430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34799825	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34816304	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34976588	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35109637	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35688814	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35856198	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35889396	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35967780	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36160284	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776978	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797898	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39626	0.97[ASN][1000 genomes]
rs40591	0.98[ASN][1000 genomes]
rs4293894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55661202	0.84[EUR][1000 genomes]
rs58825743	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59360125	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59568430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151846	0.81[EUR][1000 genomes]
rs6151888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151907	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151919	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151923	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66821541	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67240890	0.84[EUR][1000 genomes]
rs6863363	0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6874051	0.84[EUR][1000 genomes]
rs6874652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6877065	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6891635	0.82[EUR][1000 genomes]
rs701388	0.89[ASN][1000 genomes]
rs71636248	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767323	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72767330	0.84[EUR][1000 genomes]
rs7707965	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7708096	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7717404	0.84[EUR][1000 genomes]
rs7721813	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9293824	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
3	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
4	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
6	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:80089600-80118400	Weak transcription	NHEK	skin
14	chr5:80089800-80112400	Weak transcription	K562	blood
15	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:80091000-80116600	Weak transcription	A549	lung
21	chr5:80091200-80116000	Weak transcription	Brain Substantia Nigra	brain
22	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:80091400-80114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:80091400-80114800	Weak transcription	Thymus	Thymus
25	chr5:80091400-80117600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:80091400-80118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
31	chr5:80091800-80125200	Weak transcription	Osteobl	bone
32	chr5:80093000-80124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:80093800-80123800	Weak transcription	Pancreas	Pancrea
34	chr5:80094800-80124000	Weak transcription	GM12878-XiMat	blood
35	chr5:80095000-80113000	Weak transcription	Lung	lung
36	chr5:80095200-80115400	Weak transcription	Psoas Muscle	Psoas
37	chr5:80095200-80116600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:80096600-80118400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:80097000-80124400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:80097600-80121400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:80097600-80121600	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:80097800-80121600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:80098400-80121600	Weak transcription	Brain Anterior Caudate	brain
44	chr5:80099200-80117200	Weak transcription	Fetal Brain Male	brain
45	chr5:80099200-80121400	Weak transcription	Fetal Lung	lung
46	chr5:80100400-80118400	Weak transcription	HMEC	breast
47	chr5:80103000-80118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:80103800-80118400	Weak transcription	Ovary	ovary
49	chr5:80103800-80144600	Weak transcription	Gastric	stomach
50	chr5:80106400-80119400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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