Variant report

Variant	rs2466299
Chromosome Location	chr8:118183587-118183588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10101934	0.85[ASN][1000 genomes]
rs13267156	0.80[ASN][1000 genomes]
rs2464573	0.90[ASN][1000 genomes]
rs2464574	0.83[EUR][1000 genomes]
rs2464576	0.83[EUR][1000 genomes]
rs2464577	0.83[EUR][1000 genomes]
rs2464578	0.86[EUR][1000 genomes]
rs2464579	0.86[EUR][1000 genomes]
rs2464582	0.85[EUR][1000 genomes]
rs2464583	0.85[EUR][1000 genomes]
rs2464591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2464592	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2464597	0.86[EUR][1000 genomes]
rs2466290	0.86[EUR][1000 genomes]
rs2466291	0.95[ASN][1000 genomes]
rs2466292	0.96[ASN][1000 genomes]
rs2466294	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs2466295	0.81[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2466296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2466297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2466298	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2466300	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2466309	0.89[ASN][1000 genomes]
rs2466310	0.83[EUR][1000 genomes]
rs2466311	0.89[ASN][1000 genomes]
rs2466313	0.83[EUR][1000 genomes]
rs2466314	0.83[EUR][1000 genomes]
rs2466316	0.85[EUR][1000 genomes]
rs2466318	0.92[ASN][1000 genomes]
rs2466320	0.91[ASN][1000 genomes]
rs2466321	0.85[EUR][1000 genomes]
rs2466323	0.85[EUR][1000 genomes]
rs2466324	0.85[EUR][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	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1031711	chr8:118134669-118322562	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1027039	chr8:118143762-118460954	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2466299	EXT1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118178400-118184200	Weak transcription	Aorta	Aorta
2	chr8:118178800-118185600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr8:118179400-118184200	Weak transcription	Fetal Lung	lung
4	chr8:118181400-118183600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:118181400-118184200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:118182600-118185400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:118182800-118184200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:118182800-118184800	Enhancers	Brain Germinal Matrix	brain
9	chr8:118183000-118184400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:118183000-118184600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr8:118183000-118185000	Enhancers	Fetal Intestine Small	intestine
12	chr8:118183000-118186000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:118183200-118185000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:118183200-118185200	Enhancers	Fetal Intestine Large	intestine
15	chr8:118183400-118183600	Enhancers	Rectal Smooth Muscle	rectum
16	chr8:118183400-118184800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr8:118183400-118185000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr8:118183400-118185000	Enhancers	Fetal Brain Female	brain
19	chr8:118183400-118185200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr8:118183400-118185200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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