Variant report

Variant	rs4711078
Chromosome Location	chr6:25096246-25096247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1002596	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159988	0.85[ASN][1000 genomes]
rs167329	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1923195	0.82[ASN][1000 genomes]
rs2145769	0.81[ASN][1000 genomes]
rs2166682	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166683	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2295737	0.82[ASN][1000 genomes]
rs2394363	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894033	0.82[ASN][1000 genomes]
rs302966	0.81[ASN][1000 genomes]
rs302976	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs302980	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs302987	0.85[ASN][1000 genomes]
rs302990	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs303004	0.85[ASN][1000 genomes]
rs303006	0.85[ASN][1000 genomes]
rs303007	0.85[ASN][1000 genomes]
rs303008	0.85[ASN][1000 genomes]
rs303009	0.85[ASN][1000 genomes]
rs303016	0.81[ASN][1000 genomes]
rs303018	0.81[ASN][1000 genomes]
rs3792970	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792986	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812105	0.82[ASN][1000 genomes]
rs3818268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs391626	0.85[ASN][1000 genomes]
rs392852	0.90[ASN][1000 genomes]
rs398672	0.85[ASN][1000 genomes]
rs420369	0.85[ASN][1000 genomes]
rs456816	0.84[EUR][1000 genomes]
rs4711077	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712887	0.82[ASN][1000 genomes]
rs6906102	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6919920	0.82[ASN][1000 genomes]
rs715426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs715427	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740661	0.82[ASN][1000 genomes]
rs7740668	0.82[ASN][1000 genomes]
rs7773802	0.82[ASN][1000 genomes]
rs9295646	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9356961	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358833	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9379717	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9393616	0.80[ASN][1000 genomes]
rs9393617	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9654585	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4711078	CMAHP	cis	Thyroid	GTEx
rs4711078	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs4711078	CMAH	cis	multi-tissue	Pritchard
rs4711078	CMAHP	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
4	chr6:25084800-25113800	Weak transcription	Gastric	stomach
5	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
7	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
8	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
10	chr6:25087400-25098200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
13	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
15	chr6:25087800-25097200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:25088400-25096600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:25088400-25105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:25088400-25113800	Strong transcription	Dnd41	blood
20	chr6:25088600-25098000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr6:25089200-25106000	Weak transcription	Osteobl	bone
22	chr6:25089200-25108400	Weak transcription	HSMM	muscle
23	chr6:25089800-25103600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:25090000-25098200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:25090000-25098400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:25090200-25097600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:25090400-25103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:25090400-25105400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:25091400-25097600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr6:25091600-25103600	Weak transcription	HSMMtube	muscle
31	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:25091800-25103600	Weak transcription	Psoas Muscle	Psoas
33	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
34	chr6:25092800-25098000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr6:25093000-25096400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr6:25093000-25096400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr6:25093000-25096600	Strong transcription	Adipose Nuclei	Adipose
38	chr6:25093000-25097000	Strong transcription	Lung	lung
39	chr6:25093000-25097200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:25093400-25100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:25093400-25106800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:25093600-25102800	Weak transcription	Left Ventricle	heart
43	chr6:25094200-25105800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:25094800-25096800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:25095000-25096400	Strong transcription	Aorta	Aorta
46	chr6:25095000-25096600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:25095000-25097200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:25095200-25096400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:25095200-25097000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:25095200-25097000	Strong transcription	Liver	Liver

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