Variant report

Variant	rs6719727
Chromosome Location	chr2:40270608-40270609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-2	chr2:40270558-40270682	ENSG00000227028.1

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11686249	0.90[ASN][1000 genomes]
rs11690334	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs11903990	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12105254	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12473190	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12475578	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12616013	0.86[ASN][1000 genomes]
rs12617280	0.87[ASN][1000 genomes]
rs12986818	0.83[ASN][1000 genomes]
rs13025594	0.81[CHB][hapmap];0.93[ASN][1000 genomes]
rs17024771	0.83[EUR][1000 genomes]
rs17024886	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17024958	0.93[ASN][1000 genomes]
rs2192724	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2373788	0.90[ASN][1000 genomes]
rs4952638	0.83[ASN][1000 genomes]
rs6705665	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6705905	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6706273	0.97[ASN][1000 genomes]
rs6714077	0.98[ASN][1000 genomes]
rs6719947	1.00[ASN][1000 genomes]
rs6727414	0.98[ASN][1000 genomes]
rs6746945	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7568579	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586183	1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873900	chr2:40202505-40278909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv581501	chr2:40256218-40285145	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40266600-40270800	Enhancers	NHLF	lung
2	chr2:40268000-40271000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:40268200-40270800	Enhancers	Fetal Muscle Leg	muscle
4	chr2:40268200-40271800	Enhancers	NHDF-Ad	bronchial
5	chr2:40268400-40271000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:40268600-40270800	Enhancers	NH-A	brain
7	chr2:40269400-40299200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:40270200-40272000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:40270200-40272000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:40270200-40272200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:40270400-40270800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:40270600-40270800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:40270600-40270800	Enhancers	HSMM	muscle

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