Variant report

Variant	rs6450498
Chromosome Location	chr5:58293958-58293959
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036287	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10053177	0.82[AFR][1000 genomes]
rs10053330	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10061320	0.81[AFR][1000 genomes]
rs10063703	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10065540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10223103	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940638	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11750426	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11957827	0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs13362239	0.88[YRI][hapmap]
rs13362296	0.88[YRI][hapmap]
rs16888990	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs16888998	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1874857	0.82[AFR][1000 genomes]
rs1874858	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1874859	0.82[AFR][1000 genomes]
rs2055296	0.82[AFR][1000 genomes]
rs2055297	0.82[AFR][1000 genomes]
rs2055298	0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2291851	0.83[CHB][hapmap]
rs4469166	0.87[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4493634	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4631140	0.82[AFR][1000 genomes]
rs4699932	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700315	0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4700316	0.93[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]
rs4700317	0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs57527145	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58940834	0.82[AFR][1000 genomes]
rs62358490	0.81[AFR][1000 genomes]
rs62358491	0.82[AFR][1000 genomes]
rs62358492	0.82[AFR][1000 genomes]
rs6876057	0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7723432	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7727206	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7735570	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs9283720	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9292184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292187	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292188	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9292189	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58268400-58294400	Weak transcription	NH-A	brain
2	chr5:58268800-58294600	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:58270800-58295800	Weak transcription	Small Intestine	intestine
5	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:58271000-58294600	Weak transcription	Brain Angular Gyrus	brain
7	chr5:58271600-58294400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:58273000-58294400	Weak transcription	Brain Anterior Caudate	brain
9	chr5:58273800-58294400	Weak transcription	Brain Substantia Nigra	brain
10	chr5:58277800-58295600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:58278400-58297400	Weak transcription	HSMMtube	muscle
12	chr5:58278400-58299000	Weak transcription	Gastric	stomach
13	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
14	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
16	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:58280200-58297000	Weak transcription	Fetal Heart	heart
18	chr5:58280200-58297000	Weak transcription	Fetal Kidney	kidney
19	chr5:58280200-58297200	Weak transcription	Psoas Muscle	Psoas
20	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
21	chr5:58280400-58297600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:58281800-58321600	Weak transcription	Osteobl	bone
23	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
24	chr5:58284000-58296200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:58284400-58297600	Weak transcription	Fetal Lung	lung
26	chr5:58284400-58299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:58286200-58294000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:58286200-58297000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr5:58286200-58298400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:58286200-58312800	Weak transcription	Lung	lung
31	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
34	chr5:58286400-58295800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:58286600-58297400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:58286600-58298200	Weak transcription	Left Ventricle	heart
37	chr5:58286800-58295600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:58286800-58295600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
41	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:58287000-58298200	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:58287200-58294400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:58287200-58297400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:58287200-58298400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr5:58287400-58301600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:58287600-58297000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:58288600-58295600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:58288800-58297400	Weak transcription	Hela-S3	cervix
50	chr5:58288800-58297600	Weak transcription	HSMM	muscle

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