Variant report

Variant	rs4274138
Chromosome Location	chr10:91571318-91571319
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10430645	0.88[CEU][hapmap]
rs10430646	0.89[CEU][hapmap]
rs1048057	0.87[CEU][hapmap]
rs10509579	0.88[CEU][hapmap]
rs1062465	0.88[CEU][hapmap]
rs10748527	0.96[EUR][1000 genomes]
rs10785896	0.83[CEU][hapmap]
rs10785903	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10785904	0.96[EUR][1000 genomes]
rs10785905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785906	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785907	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10881614	0.82[CEU][hapmap]
rs10881618	0.82[CEU][hapmap]
rs10881619	0.83[CEU][hapmap]
rs10881628	0.89[CEU][hapmap]
rs10881629	0.89[CEU][hapmap]
rs10881631	0.89[CEU][hapmap]
rs10881646	0.81[CEU][hapmap]
rs10881647	0.87[CEU][hapmap]
rs10881664	0.88[CEU][hapmap]
rs10881666	0.88[CEU][hapmap]
rs10881671	0.85[EUR][1000 genomes]
rs10881673	0.96[EUR][1000 genomes]
rs10881674	0.96[EUR][1000 genomes]
rs10881675	0.96[EUR][1000 genomes]
rs10881677	0.96[EUR][1000 genomes]
rs10881678	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs10881679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185825	0.82[CEU][hapmap]
rs11185850	0.82[EUR][1000 genomes]
rs11185861	0.89[CEU][hapmap]
rs11185866	0.81[JPT][hapmap]
rs11185880	0.86[CEU][hapmap]
rs11185882	0.96[EUR][1000 genomes]
rs11185887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185888	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11185890	0.90[EUR][1000 genomes]
rs11185892	0.81[EUR][1000 genomes]
rs11816741	0.83[CEU][hapmap]
rs12250365	0.88[CEU][hapmap]
rs12767644	0.83[CEU][hapmap]
rs1324699	0.96[EUR][1000 genomes]
rs1324700	0.96[EUR][1000 genomes]
rs1326196	0.99[ASN][1000 genomes]
rs1409318	0.96[EUR][1000 genomes]
rs1409319	0.96[EUR][1000 genomes]
rs1409358	0.82[CEU][hapmap]
rs1555868	0.89[CEU][hapmap]
rs1886997	0.88[CEU][hapmap]
rs1998644	0.96[EUR][1000 genomes]
rs1998645	0.96[EUR][1000 genomes]
rs2026550	0.89[CEU][hapmap]
rs2077946	0.82[CEU][hapmap]
rs2182396	0.88[CEU][hapmap]
rs2419057	0.96[EUR][1000 genomes]
rs2419085	0.96[EUR][1000 genomes]
rs2900802	0.96[EUR][1000 genomes]
rs2900813	0.96[EUR][1000 genomes]
rs3740037	0.88[CEU][hapmap]
rs3758385	0.89[CEU][hapmap]
rs3824609	0.88[CEU][hapmap]
rs4934498	0.96[EUR][1000 genomes]
rs4934501	0.96[EUR][1000 genomes]
rs4934502	0.95[EUR][1000 genomes]
rs4934503	0.96[EUR][1000 genomes]
rs55772495	0.85[EUR][1000 genomes]
rs6586218	0.89[CEU][hapmap]
rs7076259	0.82[CEU][hapmap]
rs7077349	0.89[CEU][hapmap]
rs7081362	0.89[CEU][hapmap]
rs7083066	0.96[EUR][1000 genomes]
rs7085805	0.89[CEU][hapmap]
rs7087240	0.83[CEU][hapmap]
rs7087738	0.96[EUR][1000 genomes]
rs7087789	0.82[CEU][hapmap]
rs7088104	0.82[CEU][hapmap]
rs7089473	0.89[CEU][hapmap]
rs7092444	0.88[CEU][hapmap]
rs7095818	0.88[CEU][hapmap]
rs7096466	0.88[CEU][hapmap]
rs7097496	0.83[CEU][hapmap]
rs7100603	0.82[CEU][hapmap]
rs7100756	0.96[EUR][1000 genomes]
rs716781	0.83[CEU][hapmap]
rs727427	0.83[CEU][hapmap]
rs7894081	0.94[EUR][1000 genomes]
rs7895379	0.88[CEU][hapmap]
rs7898670	0.88[CEU][hapmap]
rs7902875	0.85[EUR][1000 genomes]
rs7907852	0.82[CEU][hapmap]
rs7909550	0.88[CEU][hapmap]
rs7912464	0.83[CEU][hapmap]
rs7913109	0.96[EUR][1000 genomes]
rs7924196	0.96[EUR][1000 genomes]
rs8181361	0.87[CEU][hapmap]
rs8181406	0.88[CEU][hapmap]
rs913033	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9325443	0.82[CEU][hapmap]
rs9325444	0.83[CEU][hapmap]
rs962524	0.88[CEU][hapmap]
rs9663129	0.89[CEU][hapmap]
rs9665314	0.96[EUR][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	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4274138	RP11-248C1.3	cis	Artery Tibial	GTEx
rs4274138	LINC00865	cis	Nerve Tibial	GTEx
rs4274138	LINC00865	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91569000-91573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:91569000-91573400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:91569000-91573400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr10:91569000-91573400	Weak transcription	GM12878-XiMat	blood
5	chr10:91569000-91574200	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:91571000-91571400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr10:91571000-91571600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:91571200-91571600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:91571200-91571600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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