Variant report

Variant	rs458664
Chromosome Location	chr6:25055165-25055166
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs177356	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186237	0.83[CHD][hapmap]
rs303878	0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs304256	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304257	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304258	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304259	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516361	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608874	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609408	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs458664	CMAH	cis	parietal	SCAN
rs458664	CMAH	cis	cerebellum	SCAN
rs458664	HIST1H2AA	cis	parietal	SCAN
rs458664	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs458664	CMAH	cis	lymphoblastoid	seeQTL
rs458664	HIST1H2AG	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:25049600-25058200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:25049600-25059200	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:25049800-25056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:25049800-25056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:25050000-25056200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr6:25050200-25057800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:25050200-25058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:25050200-25058200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:25050400-25056000	Weak transcription	Thymus	Thymus
11	chr6:25050600-25055400	Enhancers	Placenta	Placenta
12	chr6:25050600-25059200	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:25051200-25056000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:25051200-25056200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:25051200-25061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:25051400-25056000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:25051400-25056200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:25051600-25056000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:25051600-25056000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:25052200-25055400	Enhancers	NHLF	lung
21	chr6:25052600-25056000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:25052600-25056200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:25052800-25055400	Weak transcription	Dnd41	blood
24	chr6:25053400-25055400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:25053400-25056000	Enhancers	Primary B cells from cord blood	blood
26	chr6:25053400-25056800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:25053600-25055200	Enhancers	Rectal Smooth Muscle	rectum
28	chr6:25053600-25055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:25053600-25056200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:25053800-25055200	Flanking Active TSS	GM12878-XiMat	blood
31	chr6:25053800-25055400	Enhancers	Fetal Heart	heart
32	chr6:25053800-25055600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:25054000-25055400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:25054000-25055400	Enhancers	Colon Smooth Muscle	Colon
35	chr6:25054000-25055400	Enhancers	HSMM	muscle
36	chr6:25054000-25055400	Enhancers	HSMMtube	muscle
37	chr6:25054000-25055600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:25054000-25056000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:25054000-25056000	Weak transcription	Spleen	Spleen
40	chr6:25054000-25056400	Weak transcription	Esophagus	oesophagus
41	chr6:25054200-25055400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:25054200-25055400	Enhancers	HUVEC	blood vessel
43	chr6:25054200-25056200	Enhancers	Primary T cells from cord blood	blood
44	chr6:25054200-25061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:25054200-25061400	Weak transcription	Lung	lung
46	chr6:25054400-25055400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:25054400-25056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:25054400-25057800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:25054600-25055200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:25054600-25055200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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