Variant report

Variant	rs303008
Chromosome Location	chr6:25083528-25083529
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1002596	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs159988	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]
rs16890104	0.88[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs2028973	0.88[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2166682	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2166683	0.89[JPT][hapmap]
rs2394363	0.87[ASN][1000 genomes]
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];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs302983	0.88[JPT][hapmap]
rs302987	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs302991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.90[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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs303009	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]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.88[JPT][hapmap]
rs3792970	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792986	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3818268	0.88[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[JPT][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]
rs4711077	0.89[ASN][1000 genomes]
rs4711078	0.85[ASN][1000 genomes]
rs57304238	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57796643	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6906102	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs715426	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs715427	0.90[ASN][1000 genomes]
rs9295646	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs9295647	1.00[CHB][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]
rs9393617	1.00[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303008	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr6:25071200-25083800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:25071200-25083800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:25071200-25084000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:25071200-25084000	Weak transcription	Placenta	Placenta
8	chr6:25071200-25084000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:25071200-25084600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:25071200-25085200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:25071200-25085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:25071400-25084800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:25071400-25085600	Weak transcription	Primary B cells from cord blood	blood
14	chr6:25076200-25084200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:25077000-25086600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:25079200-25083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:25079400-25085200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:25079400-25093000	Weak transcription	Ovary	ovary
19	chr6:25079600-25086800	Weak transcription	Aorta	Aorta
20	chr6:25079800-25086800	Weak transcription	Spleen	Spleen
21	chr6:25080200-25085800	Strong transcription	Dnd41	blood
22	chr6:25080400-25084000	Weak transcription	Gastric	stomach
23	chr6:25080400-25085200	Strong transcription	Thymus	Thymus
24	chr6:25080400-25085400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:25080600-25084600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr6:25080600-25084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:25080800-25084200	Weak transcription	Lung	lung
29	chr6:25080800-25085000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:25080800-25085400	Strong transcription	Fetal Thymus	thymus
31	chr6:25081000-25086600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:25081200-25083800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:25081200-25084000	Weak transcription	Left Ventricle	heart
34	chr6:25081200-25084800	Weak transcription	Primary T cells from cord blood	blood
35	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:25081600-25084600	Weak transcription	Fetal Heart	heart
37	chr6:25081600-25088800	Weak transcription	Osteobl	bone
38	chr6:25082000-25085000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:25082200-25083800	Enhancers	HepG2	liver
40	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:25082400-25085200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr6:25082400-25085600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:25082600-25084800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:25082600-25085200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:25082800-25084400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:25082800-25086000	Weak transcription	GM12878-XiMat	blood
48	chr6:25083000-25084400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:25083000-25086000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:25083000-25086800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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