Variant report

Variant	rs272494
Chromosome Location	chr1:86816987-86816988
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493789	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10747328	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873777	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1158505	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1182102	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1334143	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1334146	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1334147	0.87[ASN][1000 genomes]
rs1334148	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs166626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166627	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129078	0.86[ASN][1000 genomes]
rs175363	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187971	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1931363	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2104963	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2151708	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151709	0.87[ASN][1000 genomes]
rs272491	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272492	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272498	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272504	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272507	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272510	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs272511	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272516	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765975	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405424	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4288573	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61804060	0.86[ASN][1000 genomes]
rs6695671	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883200	0.81[EUR][1000 genomes];0.88[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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1792405	chr1:86814270-86825639	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86805400-86817400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:86806400-86823600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:86810400-86819200	Weak transcription	NHLF	lung
5	chr1:86810600-86819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:86810800-86817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:86810800-86818600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:86810800-86819400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:86811000-86817400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:86811000-86817800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:86811200-86818800	Weak transcription	Fetal Thymus	thymus
12	chr1:86811200-86819000	Weak transcription	Fetal Lung	lung
13	chr1:86811400-86817400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:86811400-86817600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:86811600-86819000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:86812000-86818400	Weak transcription	NH-A	brain
17	chr1:86812000-86819200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:86812600-86817600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:86813000-86819200	Weak transcription	Left Ventricle	heart
20	chr1:86813200-86819200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:86813600-86818000	Weak transcription	HSMM	muscle
22	chr1:86813600-86819400	Weak transcription	Osteobl	bone
23	chr1:86813800-86817600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:86813800-86836400	Weak transcription	Lung	lung
25	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
26	chr1:86814000-86817200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:86814000-86817600	Weak transcription	NHDF-Ad	bronchial
28	chr1:86814800-86817400	Weak transcription	Dnd41	blood
29	chr1:86815000-86817600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:86815000-86819000	Weak transcription	Fetal Intestine Large	intestine
31	chr1:86815200-86817600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:86815200-86819000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
34	chr1:86815400-86817600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:86815600-86817400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:86815600-86819400	Weak transcription	Aorta	Aorta
37	chr1:86815800-86817400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:86815800-86817400	Weak transcription	HUVEC	blood vessel
39	chr1:86815800-86817600	Weak transcription	Liver	Liver
40	chr1:86815800-86817800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:86816000-86817600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:86816000-86817600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:86816000-86817600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:86816000-86817600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:86816000-86819200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:86816000-86819400	Weak transcription	Brain Germinal Matrix	brain
47	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:86816200-86817600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:86816200-86819200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:86816200-86824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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