Variant report

Variant	rs4597342
Chromosome Location	chr16:31343769-31343770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31341937..31343785-chr16:31345527..31347045,2	K562	blood:
2	chr16:31308392..31310591-chr16:31341817..31344039,2	K562	blood:
3	chr16:31198991..31202851-chr16:31343045..31346880,4	K562	blood:
4	chr16:31342392..31343986-chr16:31347244..31349142,2	MCF-7	breast:
5	chr16:31225253..31228025-chr16:31342774..31345764,2	MCF-7	breast:
6	chr16:31211282..31213179-chr16:31343243..31345626,2	K562	blood:
7	chr16:31190368..31193316-chr16:31342467..31345225,2	K562	blood:
8	chr16:31331494..31335412-chr16:31342610..31345111,3	K562	blood:
9	chr16:31118693..31121313-chr16:31341607..31344535,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COX6A2-4	chr16:31343328-31344118	NONHSAT141894

No data

Variant related genes	Relation type
ENSG00000252809	Chromatin interaction
ENSG00000177238	Chromatin interaction
ENSG00000103507	Chromatin interaction
ENSG00000169900	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10747210	0.87[ASN][1000 genomes]
rs10782004	0.92[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1106398	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs11150610	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11150611	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11150612	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11150613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11150614	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11150616	0.90[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1143682	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11574630	0.93[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11574631	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11574639	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11641202	0.92[ASN][1000 genomes]
rs11641624	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs11642120	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11645526	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs11645917	0.89[ASN][1000 genomes]
rs11859274	0.89[ASN][1000 genomes]
rs11863627	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12597154	0.89[ASN][1000 genomes]
rs12600286	0.83[ASN][1000 genomes]
rs12923297	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs12935192	0.89[ASN][1000 genomes]
rs13332545	0.84[JPT][hapmap]
rs13338928	0.97[ASN][1000 genomes]
rs2011491	0.84[EUR][1000 genomes]
rs2359661	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs28372932	0.95[ASN][1000 genomes]
rs3087796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36100148	0.97[ASN][1000 genomes]
rs3764327	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs3815801	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs3925074	0.94[ASN][1000 genomes]
rs3925075	0.94[ASN][1000 genomes]
rs4075052	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41440449	0.95[ASN][1000 genomes]
rs4261553	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4280256	0.80[ASN][1000 genomes]
rs4359460	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4411512	0.93[ASN][1000 genomes]
rs4448960	0.94[ASN][1000 genomes]
rs4450409	0.86[ASN][1000 genomes]
rs4459557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4493054	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4506917	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4594268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4608351	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889543	0.96[ASN][1000 genomes]
rs4889640	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs4889644	0.80[EUR][1000 genomes]
rs4889647	0.91[ASN][1000 genomes]
rs4889649	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs55742763	0.96[ASN][1000 genomes]
rs55912556	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56392848	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57202326	0.86[ASN][1000 genomes]
rs59338016	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61194152	0.88[ASN][1000 genomes]
rs62051517	0.97[ASN][1000 genomes]
rs6565225	0.87[EUR][1000 genomes]
rs7190997	0.86[CHB][hapmap]
rs7192161	0.91[ASN][1000 genomes]
rs7192375	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7193943	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7195915	0.97[ASN][1000 genomes]
rs7195945	0.97[ASN][1000 genomes]
rs7203472	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7206295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7499192	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs7501207	0.82[ASN][1000 genomes]
rs8048583	0.93[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs8052324	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8057320	0.86[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs8058882	0.86[ASN][1000 genomes]
rs8060268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062159	0.86[ASN][1000 genomes]
rs929868	0.84[EUR][1000 genomes]
rs9673398	0.93[ASN][1000 genomes]
rs9673404	0.92[ASN][1000 genomes]
rs9673405	0.94[ASN][1000 genomes]
rs9673519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9673522	0.94[ASN][1000 genomes]
rs9674009	0.94[ASN][1000 genomes]
rs9888907	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9938177	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4597342	VKORC1	cis	cerebellum	SCAN
rs4597342	MYST1	cis	cerebellum	SCAN
rs4597342	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx
rs4597342	FUS	cis	cerebellum	SCAN
rs4597342	MYST1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31323000-31344600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:31342800-31344200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr16:31342800-31344400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
5	chr16:31343200-31343800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:31343200-31344000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
7	chr16:31343200-31344400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:31343200-31345000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:31343200-31345000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr16:31343200-31345000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr16:31343200-31345400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr16:31343400-31344200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr16:31343400-31344600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr16:31343400-31344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:31343400-31345000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr16:31343400-31345000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:31343400-31345000	Weak transcription	Gastric	stomach
18	chr16:31343600-31344000	Strong transcription	Spleen	Spleen
19	chr16:31343600-31345000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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