Variant report

Variant	rs4074590
Chromosome Location	chr17:33671466-33671467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLFN5-2	chr17:33671250-33671583	NONHSAT053085

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1000457	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1081681	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11080339	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080341	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080342	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080343	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11869519	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12449840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451576	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1399284	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1514490	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533329	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554043	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554045	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949263	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961017	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2376046	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2928997	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35716910	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3902986	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074591	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503848	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4796074	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6505458	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6505459	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6505461	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6505462	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7209244	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7211671	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7215259	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7219864	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7220501	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs772104	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8079268	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9893160	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9904880	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9915102	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers 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 miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv457724	chr17:33609247-33691409	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv574742	chr17:33609247-33691409	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv457725	chr17:33664044-33774159	Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv574743	chr17:33664044-33774159	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv515566	chr17:33664818-33768199	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1066569	chr17:33671156-33758566	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1062610	chr17:33671466-33758566	Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4074590	NEK8	cis	parietal	SCAN
rs4074590	UTP6	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33668000-33672400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr17:33669200-33672200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:33669200-33672400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr17:33669200-33672400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:33669400-33672200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:33669600-33672200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:33669800-33672200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:33669800-33672400	Weak transcription	Dnd41	blood
9	chr17:33670000-33672200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:33670000-33672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:33670000-33672600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:33670000-33672600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:33670200-33671800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:33670400-33671600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr17:33670600-33672200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:33671200-33671600	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr17:33671200-33671600	Bivalent Enhancer	Left Ventricle	heart
18	chr17:33671200-33671800	Enhancers	Spleen	Spleen
19	chr17:33671200-33672600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr17:33671400-33671600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:33671400-33671600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
22	chr17:33671400-33671600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr17:33671400-33672400	Weak transcription	Gastric	stomach

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