Variant report

Variant	rs1874858
Chromosome Location	chr5:58313560-58313561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10052704	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10053177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10061320	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063703	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065498	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065540	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10067196	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10069187	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10223103	0.82[AFR][1000 genomes]
rs10940638	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11750426	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948356	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957827	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13357540	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13361043	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362239	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13362296	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16888990	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16888998	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874859	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055296	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055297	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2055298	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291851	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291852	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4279300	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4469166	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493634	0.81[ASN][1000 genomes]
rs4631140	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699932	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700315	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700316	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57527145	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs58779089	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58940834	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61511922	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358484	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62358490	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62358491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358492	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450498	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6876057	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6888474	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7714489	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7723432	0.87[CHB][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs7727206	0.87[CHB][hapmap];0.81[CHD][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs7729722	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7733884	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7735570	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283720	0.87[CHB][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs9292184	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9292186	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9292187	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9292188	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9292189	0.87[CHB][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
4	chr5:58281800-58321600	Weak transcription	Osteobl	bone
5	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
8	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
10	chr5:58298600-58317800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:58299600-58316600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:58299800-58318000	Weak transcription	Right Ventricle	heart
13	chr5:58302000-58315200	Weak transcription	Psoas Muscle	Psoas
14	chr5:58302400-58316200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:58302400-58321600	Weak transcription	Gastric	stomach
16	chr5:58302800-58315200	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:58303600-58317800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:58304000-58316800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:58304000-58316800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:58305800-58315400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:58307000-58322000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:58309000-58314200	Weak transcription	Fetal Heart	heart
23	chr5:58310800-58323400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:58311800-58314600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:58312000-58315000	Genic enhancers	A549	lung
26	chr5:58312200-58314000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:58312200-58314200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:58312200-58314200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:58312200-58315400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:58312400-58314200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:58312400-58314800	Strong transcription	Primary T cells from cord blood	blood
32	chr5:58312400-58315600	Strong transcription	Hela-S3	cervix
33	chr5:58312400-58316000	Strong transcription	HSMM	muscle
34	chr5:58312600-58313800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:58312600-58315200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:58312600-58316600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:58312800-58314200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:58313000-58314400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:58313000-58315400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:58313000-58317600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:58313000-58333400	Weak transcription	Lung	lung
42	chr5:58313200-58314000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:58313200-58314600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:58313200-58314800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:58313200-58316600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:58313200-58316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:58313200-58325600	Weak transcription	Fetal Lung	lung
48	chr5:58313200-58330200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:58313400-58313800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:58313400-58314000	Weak transcription	Fetal Thymus	thymus

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