Variant report

Variant	rs499385
Chromosome Location	chr1:225745557-225745558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10799310	0.81[EUR][1000 genomes]
rs10915853	0.80[AMR][1000 genomes]
rs12071529	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1222439	0.95[EUR][1000 genomes]
rs1336480	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629896	0.88[TSI][hapmap]
rs1764345	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771318	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1890999	0.85[EUR][1000 genomes]
rs2035916	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3904084	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs4233220	0.81[EUR][1000 genomes]
rs475794	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481746	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516323	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525062	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526221	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552106	0.82[AMR][1000 genomes]
rs566085	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59363938	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426075	0.89[TSI][hapmap]
rs6692054	0.81[EUR][1000 genomes]
rs72750896	0.88[EUR][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9651009	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
2	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:225707200-225755000	Weak transcription	Gastric	stomach
4	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
6	chr1:225717800-225758200	Weak transcription	HepG2	liver
7	chr1:225718400-225756400	Weak transcription	NHLF	lung
8	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:225727600-225753600	Weak transcription	NHEK	skin
12	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
15	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
19	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:225735400-225746000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:225736600-225753400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:225736600-225756200	Weak transcription	HSMMtube	muscle
24	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
25	chr1:225738000-225747200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:225738000-225753600	Weak transcription	Aorta	Aorta
27	chr1:225738000-225753600	Weak transcription	Ovary	ovary
28	chr1:225738200-225753400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:225738400-225745800	Weak transcription	Fetal Heart	heart
30	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
31	chr1:225739800-225753200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:225739800-225754000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:225740400-225748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:225741800-225758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225742800-225746800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:225742800-225753600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:225743200-225745800	Weak transcription	Osteobl	bone
38	chr1:225743200-225748400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:225743800-225747800	Strong transcription	NH-A	brain
40	chr1:225743800-225748600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:225744000-225746200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr1:225744000-225747800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:225744000-225748800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:225744200-225747800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:225744400-225745800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr1:225744400-225746000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:225744400-225746200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr1:225744400-225747800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:225744600-225750600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:225744800-225746000	Strong transcription	Fetal Lung	lung

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