Variant report

Variant	rs6603973
Chromosome Location	chr1:92933626-92933627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPAP2-3	chr1:92933167-92933655	NONHSAT004458

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10874637	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164226	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164312	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11577572	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11577839	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11578012	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11578098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578400	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11580693	0.85[EUR][1000 genomes]
rs11581176	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11585255	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11586355	0.85[EUR][1000 genomes]
rs11586989	0.85[EUR][1000 genomes]
rs11588044	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11588153	0.85[EUR][1000 genomes]
rs11589122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11589858	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11800771	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11800848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11804321	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11805007	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11808092	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12094293	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12401372	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12404806	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12407622	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12411162	0.85[EUR][1000 genomes]
rs12727665	0.83[ASN][1000 genomes]
rs12731923	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12735898	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12740246	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs12743520	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12749317	0.86[EUR][1000 genomes]
rs12755781	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12756786	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12757533	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12759512	0.83[ASN][1000 genomes]
rs1325435	0.88[ASN][1000 genomes]
rs1384612	0.83[ASN][1000 genomes]
rs1384613	0.83[ASN][1000 genomes]
rs1415296	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17519385	0.83[ASN][1000 genomes]
rs17519972	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap]
rs17578686	0.83[ASN][1000 genomes]
rs1809606	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2004814	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069051	0.83[ASN][1000 genomes]
rs2391158	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2391162	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34090353	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35015161	0.83[ASN][1000 genomes]
rs35580949	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3790450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41286801	0.86[ASN][1000 genomes]
rs41313373	0.86[ASN][1000 genomes]
rs4642892	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4658297	0.85[EUR][1000 genomes]
rs4658298	0.85[EUR][1000 genomes]
rs4658299	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs4949888	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970699	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970713	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58394161	1.00[ASN][1000 genomes]
rs6603974	1.00[ASN][1000 genomes]
rs6660889	0.86[ASN][1000 genomes]
rs6662379	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6662618	0.83[ASN][1000 genomes]
rs6663905	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66758257	0.85[EUR][1000 genomes]
rs6689470	0.86[ASN][1000 genomes]
rs72720457	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72722469	0.86[ASN][1000 genomes]
rs72722475	0.86[ASN][1000 genomes]
rs72722484	0.86[ASN][1000 genomes]
rs7511669	0.83[ASN][1000 genomes]
rs7520275	1.00[JPT][hapmap]
rs7522081	0.83[ASN][1000 genomes]
rs7524120	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7550680	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554154	0.88[ASN][1000 genomes]
rs912794	0.83[ASN][1000 genomes]
rs9439911	0.87[EUR][1000 genomes];0.83[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	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6603973	ZNF326	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92925600-92946000	Weak transcription	Right Atrium	heart
2	chr1:92926200-92934200	Enhancers	Dnd41	blood
3	chr1:92929400-92940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:92929600-92940800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:92930600-92939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:92930600-92939400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:92930800-92944400	Weak transcription	Spleen	Spleen
8	chr1:92931000-92939000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:92931000-92939000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:92931400-92935000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:92933000-92939600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:92933000-92939800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:92933200-92938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:92933400-92938600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:92933400-92939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:92933400-92939000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:92933400-92939000	Weak transcription	Thymus	Thymus
18	chr1:92933400-92941200	Weak transcription	Primary T cells from cord blood	blood
19	chr1:92933600-92934600	Weak transcription	Fetal Thymus	thymus
20	chr1:92933600-92939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:92933600-92939600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:92933600-92939800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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