Variant report

Variant	rs17536299
Chromosome Location	chr1:223096435-223096436
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10495202	0.91[AMR][1000 genomes]
rs1132369	0.91[AMR][1000 genomes]
rs1132371	0.91[AMR][1000 genomes]
rs11588378	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12734196	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17473936	1.00[MKK][hapmap]
rs17475753	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17475774	1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17477752	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534704	0.91[AMR][1000 genomes]
rs17534774	0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17535004	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17535032	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17535137	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17536056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362013	0.84[MKK][hapmap]
rs34080450	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34151467	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34194482	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34225287	0.91[AMR][1000 genomes]
rs34229647	1.00[MKK][hapmap]
rs34232799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34277924	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34299243	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34355153	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34503525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34643369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34690779	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34701716	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34713681	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34755094	0.91[AMR][1000 genomes]
rs34761499	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34774807	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34791822	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34804073	0.91[AMR][1000 genomes]
rs34893395	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34962524	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35095009	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[MKK][hapmap];0.83[ASN][1000 genomes]
rs35131473	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35197173	0.82[AMR][1000 genomes]
rs35217299	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35270996	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35283922	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35319605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35356885	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35399857	0.91[AMR][1000 genomes]
rs35506390	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35538644	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35551242	0.94[EUR][1000 genomes]
rs35578837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35597626	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35597790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35689138	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35756512	0.86[AMR][1000 genomes]
rs35773347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35898924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35912520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35947021	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032255	0.86[AMR][1000 genomes]
rs36066427	0.86[AMR][1000 genomes]
rs36090356	0.91[AMR][1000 genomes]
rs36113407	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4298738	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61838118	0.82[AMR][1000 genomes]
rs61838119	0.91[AMR][1000 genomes]
rs61839587	0.91[AMR][1000 genomes]
rs61839588	0.91[AMR][1000 genomes]
rs61839600	0.91[AMR][1000 genomes]
rs61839601	0.91[AMR][1000 genomes]
rs61839602	0.91[AMR][1000 genomes]
rs61840263	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61840271	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61840273	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71644708	0.91[AMR][1000 genomes]
rs71644709	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71644714	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71644716	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71644718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223083200-223101400	Weak transcription	Fetal Heart	heart
2	chr1:223083600-223101600	Weak transcription	Fetal Stomach	stomach
3	chr1:223090800-223101600	Weak transcription	Pancreas	Pancrea
4	chr1:223091200-223097000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:223092400-223098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:223092400-223101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:223092400-223116200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:223092800-223096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:223093000-223097200	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:223093000-223097400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:223093000-223101200	Weak transcription	Adipose Nuclei	Adipose
12	chr1:223094000-223096800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:223094000-223097000	Weak transcription	NHLF	lung
14	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:223094000-223101400	Weak transcription	HSMM	muscle
17	chr1:223094600-223099800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:223094800-223097400	Enhancers	Stomach Mucosa	stomach
19	chr1:223095000-223098000	Enhancers	Fetal Lung	lung
20	chr1:223095400-223096600	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:223095400-223098000	Enhancers	Ovary	ovary
22	chr1:223095600-223096600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:223095600-223096600	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:223095600-223099000	Weak transcription	Right Atrium	heart
25	chr1:223095600-223100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:223095600-223101400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:223095800-223097600	Weak transcription	Osteobl	bone
28	chr1:223096000-223097200	Weak transcription	HepG2	liver
29	chr1:223096000-223101400	Weak transcription	Fetal Kidney	kidney
30	chr1:223096400-223098200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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