Variant report

Variant	rs2867672
Chromosome Location	chr4:80493766-80493767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10004226	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10022663	0.84[ASN][1000 genomes]
rs1031005	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11098762	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11098764	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11098766	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11098770	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1115518	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs1115519	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs11736369	0.81[ASN][1000 genomes]
rs11941782	0.81[ASN][1000 genomes]
rs12500146	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12501981	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs12507160	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12507375	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12511646	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12643491	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12643976	0.82[AMR][1000 genomes]
rs13112067	0.81[ASN][1000 genomes]
rs13112577	0.81[ASN][1000 genomes]
rs13124357	0.80[AMR][1000 genomes]
rs13127970	0.81[ASN][1000 genomes]
rs13146986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1371993	0.81[ASN][1000 genomes]
rs1440852	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1440853	0.84[ASN][1000 genomes]
rs1440854	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1440864	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1837645	0.81[ASN][1000 genomes]
rs1837646	0.81[ASN][1000 genomes]
rs1975399	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2165386	0.84[ASN][1000 genomes]
rs2165387	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35019476	0.80[AMR][1000 genomes]
rs3943669	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4389603	0.84[ASN][1000 genomes]
rs4583785	0.81[AMR][1000 genomes]
rs4586978	0.81[AMR][1000 genomes]
rs4975056	0.81[ASN][1000 genomes]
rs4975057	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4975089	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs6812760	0.81[ASN][1000 genomes]
rs6850999	0.84[ASN][1000 genomes]
rs6852514	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7667469	0.84[ASN][1000 genomes]
rs9307545	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs968176	0.80[AMR][1000 genomes];0.84[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2867672	LINC00989	cis	Whole Blood	GTEx
rs2867672	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80491000-80495800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:80491000-80497400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:80492400-80495600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:80493000-80495600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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