Variant report

Variant	rs2516577
Chromosome Location	chr6:25136194-25136195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1547054	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1547055	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1823184	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1838967	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1923195	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2145769	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2295737	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2894033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs302967	0.91[JPT][hapmap]
rs302968	0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302969	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302970	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302978	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs302979	0.91[JPT][hapmap]
rs302984	0.91[JPT][hapmap]
rs302986	0.86[AMR][1000 genomes]
rs302989	0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs303015	1.00[YRI][hapmap]
rs303016	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs303018	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs303022	0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs303023	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs303025	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3812105	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4712887	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6919920	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7740661	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7740668	0.90[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7773802	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7775959	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7776121	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9379721	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393613	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393616	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[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	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	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
5	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
6	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
7	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
rs2516577	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs2516577	hmm14470	cis	multi-tissue	Pritchard
rs2516577	CMAH	cis	normal skin	skin_eQTL
rs2516577	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:25113000-25136800	Weak transcription	Osteobl	bone
3	chr6:25116000-25137000	Weak transcription	Lung	lung
4	chr6:25122600-25137000	Weak transcription	Colonic Mucosa	Colon
5	chr6:25122600-25137000	Weak transcription	HSMM	muscle
6	chr6:25122800-25137000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:25123600-25136600	Weak transcription	HSMMtube	muscle
8	chr6:25123800-25136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
10	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
11	chr6:25126200-25136400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:25126400-25136800	Weak transcription	Liver	Liver
13	chr6:25129400-25136400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:25129600-25136800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:25130600-25136800	Weak transcription	Ovary	ovary
16	chr6:25131800-25136600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:25132000-25136600	ZNF genes & repeats	Dnd41	blood
18	chr6:25132400-25136800	Weak transcription	Adipose Nuclei	Adipose
19	chr6:25132800-25136600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr6:25133200-25137000	Strong transcription	Fetal Thymus	thymus
21	chr6:25133800-25136200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:25133800-25138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:25134000-25136200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:25134000-25136200	Weak transcription	Aorta	Aorta
25	chr6:25134000-25136200	Weak transcription	Left Ventricle	heart
26	chr6:25134000-25136800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:25134000-25137200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:25134200-25136200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:25134200-25136400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:25134200-25136400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:25134200-25136600	Weak transcription	NHDF-Ad	bronchial
32	chr6:25134200-25136800	Weak transcription	Hela-S3	cervix
33	chr6:25134600-25136200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:25134600-25136400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:25135000-25136800	Strong transcription	Placenta	Placenta
36	chr6:25135200-25136200	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr6:25135200-25136200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:25135200-25136600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:25135200-25140200	Active TSS	Right Atrium	heart
40	chr6:25135400-25136600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:25135400-25136600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:25135400-25136600	ZNF genes & repeats	Thymus	Thymus
43	chr6:25135400-25138200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:25135600-25136200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:25135600-25136200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:25135600-25136400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:25135600-25136800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:25135600-25137000	Weak transcription	Psoas Muscle	Psoas
49	chr6:25135800-25136200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:25135800-25136200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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