Variant report

Variant	rs6662067
Chromosome Location	chr1:212060792-212060793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INTS7-2	chr1:212059601-212062399	NONHSAT009336

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10863929	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119807	0.83[ASN][1000 genomes]
rs11119813	0.91[ASN][1000 genomes]
rs11487823	0.91[ASN][1000 genomes]
rs12059988	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12076991	0.91[ASN][1000 genomes]
rs12077561	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12084756	0.83[ASN][1000 genomes]
rs12085235	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12085288	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12088743	0.83[ASN][1000 genomes]
rs12090490	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12095938	0.83[ASN][1000 genomes]
rs12410970	0.83[ASN][1000 genomes]
rs28768080	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28800280	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28862981	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738197	0.91[ASN][1000 genomes]
rs3862952	0.83[ASN][1000 genomes]
rs4447046	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4537651	0.92[ASN][1000 genomes]
rs4562685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623773	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56132364	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828259	0.83[ASN][1000 genomes]
rs61828491	0.91[ASN][1000 genomes]
rs61828492	0.86[ASN][1000 genomes]
rs61828510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540709	0.91[ASN][1000 genomes]
rs6664082	0.83[ASN][1000 genomes]
rs6678582	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6684049	0.83[ASN][1000 genomes]
rs6704043	0.83[ASN][1000 genomes]
rs7518896	0.91[ASN][1000 genomes]
rs7524009	0.83[ASN][1000 genomes]
rs7534335	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762218	chr1:212046447-212087682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6662067	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212058400-212061800	Enhancers	Liver	Liver
2	chr1:212059200-212061000	Enhancers	Fetal Intestine Large	intestine
3	chr1:212059200-212061800	Enhancers	Adipose Nuclei	Adipose
4	chr1:212059400-212061800	Enhancers	GM12878-XiMat	blood
5	chr1:212059600-212061000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:212059600-212061200	Weak transcription	Pancreas	Pancrea
7	chr1:212059800-212061000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:212059800-212062000	Enhancers	HepG2	liver
9	chr1:212060000-212061200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:212060000-212062600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:212060000-212068600	Weak transcription	A549	lung
12	chr1:212060200-212062600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212060400-212061600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:212060600-212061600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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