Variant report

Variant	rs9393603
Chromosome Location	chr6:24978504-24978505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10946738	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13192546	0.82[ASN][1000 genomes]
rs13209866	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs450392	0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs62401115	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs67879608	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742953	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295637	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295638	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348651	0.82[AMR][1000 genomes]
rs9348652	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9348653	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356950	0.93[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9356951	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358809	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358810	0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9358811	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358812	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358813	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358814	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366588	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366589	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366590	0.93[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379700	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379701	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379702	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379703	0.82[ASN][1000 genomes]
rs9379704	0.82[ASN][1000 genomes]
rs9393596	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393597	0.87[ASW][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9393598	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393599	0.93[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393602	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9393603	ZSCAN16	cis	parietal	SCAN
rs9393603	HIST1H2BK	cis	cerebellum	SCAN

Chromatin state (count:40 , 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	chr6:24969200-24980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:24969400-24980600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:24973400-24979200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:24975000-24978800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:24975000-24979000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:24975000-24979200	Weak transcription	HSMM	muscle
9	chr6:24975000-24979400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:24975200-24979200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:24975400-24980600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:24975400-24980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:24975800-24978600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:24975800-24979200	Weak transcription	Primary B cells from cord blood	blood
15	chr6:24975800-24980800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:24976000-24978800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:24976000-24979000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:24976000-24979000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:24976000-24979200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:24976000-24979400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:24976000-24979800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:24976000-24980800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:24976000-24980800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:24976400-24979200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:24976400-24979200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:24976600-24981600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:24977800-24978600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:24977800-24978800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:24977800-24979400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:24977800-24980200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:24977800-24982000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr6:24977800-24982400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:24977800-24986000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:24978000-24980600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr6:24978000-24980800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:24978200-24979000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:24978200-24979400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:24978200-24980600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:24978200-24981000	Weak transcription	Ovary	ovary
40	chr6:24978400-24978800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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