Variant report

Variant	rs303009
Chromosome Location	chr6:25082540-25082541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1002596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs159988	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];1.00[ASN][1000 genomes]
rs167329	0.88[JPT][hapmap]
rs16890104	0.96[CHD][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs1923195	0.85[CHD][hapmap]
rs2028973	1.00[ASW][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2166682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2166683	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2394363	0.87[ASN][1000 genomes]
rs2894033	0.85[CHD][hapmap]
rs302966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs302973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs302976	0.88[JPT][hapmap]
rs302980	0.88[JPT][hapmap]
rs302983	0.88[JPT][hapmap]
rs302987	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs302989	0.81[CHD][hapmap]
rs302991	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303000	0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs303004	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303006	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303007	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];1.00[ASN][1000 genomes]
rs303008	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];1.00[ASN][1000 genomes]
rs303015	0.84[JPT][hapmap]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs3792970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792971	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3812105	0.88[CHD][hapmap]
rs3818268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs391626	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs398672	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456816	1.00[CHB][hapmap]
rs4711077	0.89[ASN][1000 genomes]
rs4711078	0.85[ASN][1000 genomes]
rs4712887	0.85[CHD][hapmap]
rs57304238	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57796643	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6906102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs715426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs715427	0.90[ASN][1000 genomes]
rs7740661	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7740668	0.86[CHB][hapmap]
rs9295646	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs9295647	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9356961	0.90[ASN][1000 genomes]
rs9358833	0.90[ASN][1000 genomes]
rs9379717	0.82[ASN][1000 genomes]
rs9393613	0.86[CHB][hapmap]
rs9393617	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9654585	0.90[ASN][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	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	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
4	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
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs303009	GMNN	cis	brain	seeQTL
rs303009	CMAH	cis	parietal	SCAN
rs303009	CMAH	cis	lymphoblastoid	seeQTL
rs303009	CMAH	cis	cerebellum	SCAN
rs303009	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25067600-25084600	Weak transcription	HSMMtube	muscle
2	chr6:25069800-25084000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:25071000-25084400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:25071200-25082600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:25071200-25083800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:25071200-25083800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:25071200-25084000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:25071200-25084000	Weak transcription	Placenta	Placenta
9	chr6:25071200-25084000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:25071200-25084600	Weak transcription	Adipose Nuclei	Adipose
11	chr6:25071200-25085200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:25071200-25085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:25071400-25084800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:25071400-25085600	Weak transcription	Primary B cells from cord blood	blood
15	chr6:25076200-25084200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:25077000-25086600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:25079200-25083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:25079400-25085200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:25079400-25093000	Weak transcription	Ovary	ovary
20	chr6:25079600-25086800	Weak transcription	Aorta	Aorta
21	chr6:25079800-25086800	Weak transcription	Spleen	Spleen
22	chr6:25080000-25082800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:25080200-25085800	Strong transcription	Dnd41	blood
24	chr6:25080400-25084000	Weak transcription	Gastric	stomach
25	chr6:25080400-25085200	Strong transcription	Thymus	Thymus
26	chr6:25080400-25085400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:25080600-25084600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr6:25080600-25084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:25080800-25084200	Weak transcription	Lung	lung
31	chr6:25080800-25085000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:25080800-25085400	Strong transcription	Fetal Thymus	thymus
33	chr6:25081000-25086600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:25081200-25082600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:25081200-25083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:25081200-25084000	Weak transcription	Left Ventricle	heart
37	chr6:25081200-25084800	Weak transcription	Primary T cells from cord blood	blood
38	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:25081600-25084600	Weak transcription	Fetal Heart	heart
40	chr6:25081600-25088800	Weak transcription	Osteobl	bone
41	chr6:25082000-25085000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:25082200-25083000	Enhancers	Liver	Liver
43	chr6:25082200-25083800	Enhancers	HepG2	liver
44	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:25082400-25083000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:25082400-25083200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:25082400-25085200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:25082400-25085600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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