Variant report

Variant	rs1992367
Chromosome Location	chr4:80449649-80449650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10004226	0.82[ASN][1000 genomes]
rs10021556	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10022309	0.98[ASN][1000 genomes]
rs10022314	0.98[ASN][1000 genomes]
rs10022663	0.83[ASN][1000 genomes]
rs10025630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10027904	0.84[ASN][1000 genomes]
rs10033410	0.98[ASN][1000 genomes]
rs1031005	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1074134	0.84[ASN][1000 genomes]
rs11098741	0.98[ASN][1000 genomes]
rs11098742	0.98[ASN][1000 genomes]
rs11098762	0.82[ASN][1000 genomes]
rs11098764	0.82[ASN][1000 genomes]
rs11098766	0.82[ASN][1000 genomes]
rs11098770	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1115518	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1115519	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs11728755	0.82[ASN][1000 genomes]
rs11736348	0.84[ASN][1000 genomes]
rs11736369	0.83[ASN][1000 genomes]
rs11936123	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11941782	0.86[ASN][1000 genomes]
rs12500146	0.82[ASN][1000 genomes]
rs12501981	0.95[JPT][hapmap]
rs12502224	0.98[ASN][1000 genomes]
rs12506212	0.88[ASN][1000 genomes]
rs12507160	0.82[ASN][1000 genomes]
rs12507375	0.82[ASN][1000 genomes]
rs12510204	0.98[ASN][1000 genomes]
rs12510243	0.98[ASN][1000 genomes]
rs12511646	0.82[ASN][1000 genomes]
rs12511890	0.84[ASN][1000 genomes]
rs12513177	0.98[ASN][1000 genomes]
rs12639996	0.98[ASN][1000 genomes]
rs12640638	0.98[ASN][1000 genomes]
rs12643491	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13111877	0.84[ASN][1000 genomes]
rs13112067	0.86[ASN][1000 genomes]
rs13112577	0.86[ASN][1000 genomes]
rs13118924	0.82[ASN][1000 genomes]
rs13128134	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144408	0.93[ASN][1000 genomes]
rs13146986	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1371993	0.86[ASN][1000 genomes]
rs1371996	0.99[ASN][1000 genomes]
rs1440852	0.82[ASN][1000 genomes]
rs1440853	0.82[ASN][1000 genomes]
rs1440854	0.82[ASN][1000 genomes]
rs1440860	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1440861	0.84[ASN][1000 genomes]
rs1440862	0.84[ASN][1000 genomes]
rs1440863	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1440864	0.82[ASN][1000 genomes]
rs1440865	0.98[ASN][1000 genomes]
rs1440866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561638	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1561639	0.84[ASN][1000 genomes]
rs1561640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1595966	0.98[ASN][1000 genomes]
rs1837645	0.86[ASN][1000 genomes]
rs1837646	0.86[ASN][1000 genomes]
rs1837647	0.94[ASN][1000 genomes]
rs1899232	0.84[ASN][1000 genomes]
rs1971838	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1975399	0.82[ASN][1000 genomes]
rs2119419	0.89[ASN][1000 genomes]
rs2119420	0.89[ASN][1000 genomes]
rs2119421	1.00[ASN][1000 genomes]
rs2165386	0.82[ASN][1000 genomes]
rs2165387	0.83[ASN][1000 genomes]
rs2165388	0.95[ASN][1000 genomes]
rs3943669	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4389603	0.83[ASN][1000 genomes]
rs4443312	0.86[ASN][1000 genomes]
rs4583785	0.82[ASN][1000 genomes]
rs4975052	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975053	0.98[ASN][1000 genomes]
rs4975054	0.98[ASN][1000 genomes]
rs4975055	0.98[ASN][1000 genomes]
rs4975056	0.85[ASN][1000 genomes]
rs4975057	0.83[ASN][1000 genomes]
rs4975089	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6812760	0.86[ASN][1000 genomes]
rs6850999	0.82[ASN][1000 genomes]
rs6852514	0.82[ASN][1000 genomes]
rs723243	0.84[ASN][1000 genomes]
rs723245	0.83[ASN][1000 genomes]
rs7655446	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7663844	0.84[ASN][1000 genomes]
rs7667469	0.82[ASN][1000 genomes]
rs7670107	0.84[ASN][1000 genomes]
rs7684683	0.84[ASN][1000 genomes]
rs7690520	0.86[ASN][1000 genomes]
rs7691021	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7691868	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7691918	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7697359	0.98[ASN][1000 genomes]
rs880988	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9307532	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307545	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs968176	0.82[ASN][1000 genomes]
rs998437	0.86[ASN][1000 genomes]
rs9993773	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv829980	chr4:80442108-80468775	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992367	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80448200-80453800	Weak transcription	Fetal Brain Male	brain
2	chr4:80448800-80450000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr4:80449000-80450400	Enhancers	Dnd41	blood
4	chr4:80449200-80450000	Enhancers	Primary T cells from cord blood	blood
5	chr4:80449400-80449800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:80449400-80449800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:80449400-80449800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:80449400-80449800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:80449400-80450000	Weak transcription	Fetal Brain Female	brain
10	chr4:80449400-80450000	Enhancers	Fetal Thymus	thymus

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