Variant report

Variant	rs1353258
Chromosome Location	chr5:14855659-14855660
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1061813	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133799	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117282	0.87[ASN][1000 genomes]
rs12653321	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155894	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1812658	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2453316	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258218	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258219	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs258222	0.81[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258224	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258225	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258226	0.82[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258227	0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258228	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258231	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs25957	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs28005	0.87[ASN][1000 genomes]
rs28006	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs28108	0.88[ASN][1000 genomes]
rs30615	0.82[ASN][1000 genomes]
rs31909	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs31912	0.89[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31933	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs31990	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs33102	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39636	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39916	0.83[ASN][1000 genomes]
rs42679	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42680	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs826352	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826357	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs879253	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9790982	1.00[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2753381	chr5:14814900-14882800	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	esv2755533	chr5:14814900-14882800	Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	esv2755538	chr5:14814900-14927500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14811600-14861200	Weak transcription	Colonic Mucosa	Colon
2	chr5:14824800-14869600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr5:14828800-14856200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:14830400-14866400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:14831000-14870400	Weak transcription	Spleen	Spleen
6	chr5:14835600-14869000	Weak transcription	NHDF-Ad	bronchial
7	chr5:14835800-14864200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:14837400-14869400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:14839200-14859800	Weak transcription	Aorta	Aorta
10	chr5:14840200-14864600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:14844800-14869200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:14848800-14861800	Weak transcription	Adipose Nuclei	Adipose
13	chr5:14848800-14870000	Weak transcription	Thymus	Thymus
14	chr5:14849200-14869800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:14850200-14856400	Enhancers	Fetal Intestine Large	intestine
16	chr5:14850400-14861600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:14850400-14861600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:14850600-14861200	Weak transcription	Liver	Liver
19	chr5:14850600-14863000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:14850800-14856200	Enhancers	Fetal Intestine Small	intestine
21	chr5:14850800-14861200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:14850800-14869000	Weak transcription	Brain Germinal Matrix	brain
23	chr5:14851400-14856600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:14851400-14860200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:14851400-14861400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:14851400-14863000	Weak transcription	Brain Anterior Caudate	brain
27	chr5:14851400-14863200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:14851600-14856400	Weak transcription	Osteobl	bone
29	chr5:14851600-14859600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:14851600-14860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:14851600-14860000	Weak transcription	Pancreas	Pancrea
32	chr5:14851600-14861800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:14851600-14869800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:14851800-14856200	Weak transcription	HepG2	liver
35	chr5:14851800-14859600	Weak transcription	Dnd41	blood
36	chr5:14851800-14860000	Weak transcription	Brain Angular Gyrus	brain
37	chr5:14851800-14862800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:14852400-14861400	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:14852400-14861400	Weak transcription	Gastric	stomach
40	chr5:14853200-14869000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:14854400-14856200	Enhancers	Psoas Muscle	Psoas
42	chr5:14854800-14855800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr5:14854800-14857200	Enhancers	Fetal Heart	heart
44	chr5:14854800-14863000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:14855000-14857400	Strong transcription	Primary T cells from cord blood	blood
46	chr5:14855400-14855800	Enhancers	Duodenum Mucosa	Duodenum
47	chr5:14855400-14860000	Weak transcription	Esophagus	oesophagus
48	chr5:14855400-14860000	Weak transcription	Left Ventricle	heart
49	chr5:14855400-14860000	Weak transcription	Lung	lung
50	chr5:14855400-14860000	Weak transcription	Right Atrium	heart

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