Variant report

Variant	rs9393599
Chromosome Location	chr6:24975706-24975707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10946738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs127489	0.84[ASN][1000 genomes]
rs450392	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs675188	0.81[ASN][1000 genomes]
rs67879608	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742953	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295637	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295638	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348652	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9348653	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358809	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358810	0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9358811	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358812	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358813	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358814	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366588	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366589	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379700	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379701	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379702	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393596	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393597	0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9393598	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393601	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393602	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393603	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9393599	LRRC16A	cis	lymphoblastoid	seeQTL
rs9393599	HIST1H2BK	cis	cerebellum	SCAN
rs9393599	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24954400-24980800	Weak transcription	Thymus	Thymus
3	chr6:24966600-24976000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:24969200-24980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:24969400-24980600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:24973400-24979200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:24973600-24976000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:24974000-24976000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:24974200-24975800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr6:24974200-24976000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:24974200-24976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:24974400-24976000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:24974600-24975800	Enhancers	Primary B cells from cord blood	blood
14	chr6:24974600-24976000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:24975000-24976000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:24975000-24978800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:24975000-24979000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:24975000-24979200	Weak transcription	HSMM	muscle
19	chr6:24975000-24979400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:24975200-24975800	Enhancers	GM12878-XiMat	blood
21	chr6:24975200-24976000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:24975200-24976400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:24975200-24979200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:24975400-24976000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:24975400-24980600	Weak transcription	Primary T cells from cord blood	blood
26	chr6:24975400-24980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:24975600-24975800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:24975600-24976000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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