Variant report

Variant	rs303015
Chromosome Location	chr6:25139775-25139776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1547055	1.00[YRI][hapmap]
rs159988	0.84[JPT][hapmap]
rs167329	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16890104	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2028973	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2166682	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2166683	0.84[JPT][hapmap]
rs2295737	1.00[YRI][hapmap]
rs2516577	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs302968	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302969	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302970	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs302973	0.84[JPT][hapmap]
rs302976	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs302980	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs302982	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs302983	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs302986	0.85[AMR][1000 genomes]
rs302989	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs302990	1.00[CEU][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs302991	0.84[JPT][hapmap]
rs303006	0.84[JPT][hapmap]
rs303009	0.84[JPT][hapmap]
rs303016	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303017	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs303018	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303022	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs303023	0.91[AMR][1000 genomes]
rs303024	0.87[ASN][1000 genomes]
rs303025	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs303026	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3792970	0.84[JPT][hapmap]
rs3792971	0.84[JPT][hapmap]
rs392852	0.84[JPT][hapmap]
rs4712887	1.00[YRI][hapmap]
rs6919920	1.00[YRI][hapmap]
rs9295647	0.84[JPT][hapmap]
rs9393613	1.00[YRI][hapmap]
rs9393617	0.84[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs303015	CMAH	cis	multi-tissue	Pritchard
rs303015	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25135200-25140200	Active TSS	Right Atrium	heart
2	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:25136200-25140000	Active TSS	Aorta	Aorta
5	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25136800-25140000	Active TSS	Ovary	ovary
7	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
9	chr6:25137800-25139800	Active TSS	Brain Substantia Nigra	brain
10	chr6:25137800-25139800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:25137800-25139800	Flanking Active TSS	HUVEC	blood vessel
12	chr6:25138000-25139800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr6:25138000-25140200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:25138400-25140200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:25138400-25140400	Active TSS	Fetal Intestine Large	intestine
16	chr6:25138600-25139800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr6:25138600-25140000	Active TSS	Fetal Intestine Small	intestine
18	chr6:25138800-25139800	Weak transcription	Pancreas	Pancrea
19	chr6:25138800-25140000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr6:25138800-25140200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25138800-25152800	Weak transcription	Lung	lung
22	chr6:25139000-25139800	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr6:25139200-25139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:25139200-25139800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:25139200-25139800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:25139200-25139800	Active TSS	NH-A	brain
27	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:25139400-25139800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:25139400-25139800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr6:25139400-25139800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr6:25139400-25139800	Flanking Active TSS	Liver	Liver
32	chr6:25139400-25139800	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr6:25139400-25139800	Enhancers	Fetal Heart	heart
34	chr6:25139400-25139800	Flanking Active TSS	Fetal Kidney	kidney
35	chr6:25139400-25139800	Flanking Active TSS	Fetal Lung	lung
36	chr6:25139400-25139800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:25139400-25139800	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:25139400-25139800	Flanking Active TSS	NHEK	skin
39	chr6:25139400-25139800	Flanking Active TSS	Osteobl	bone
40	chr6:25139400-25140000	Weak transcription	Right Ventricle	heart
41	chr6:25139400-25140000	Flanking Active TSS	Dnd41	blood
42	chr6:25139400-25140200	Enhancers	Fetal Brain Male	brain
43	chr6:25139600-25139800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:25139600-25139800	Enhancers	Primary T cells from cord blood	blood
45	chr6:25139600-25139800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:25139600-25139800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:25139600-25139800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr6:25139600-25139800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:25139600-25139800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:25139600-25139800	Enhancers	Primary T helper cells fromperipheralblood	blood

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