Variant report

Variant	rs4975095
Chromosome Location	chr4:80484351-80484352
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10022663	0.82[AMR][1000 genomes]
rs11941782	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12643491	0.82[AMR][1000 genomes]
rs13112067	0.82[ASN][1000 genomes]
rs13112577	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1371993	0.82[ASN][1000 genomes]
rs1440853	0.81[AMR][1000 genomes]
rs1837645	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1837646	0.82[ASN][1000 genomes]
rs2165386	0.81[AMR][1000 genomes]
rs3943669	0.81[AMR][1000 genomes]
rs4389603	0.81[AMR][1000 genomes]
rs4975056	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6812760	0.82[ASN][1000 genomes]
rs6850999	0.81[AMR][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	nsv999174	chr4:80212935-80512356	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4975095	LINC00989	cis	Whole Blood	GTEx
rs4975095	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs4975095	LINC00989	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80467600-80485600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:80481800-80490800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:80483400-80484400	Weak transcription	K562	blood
4	chr4:80483400-80490800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:80483800-80484800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:80484200-80484600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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