Variant report

Variant	rs2166683
Chromosome Location	chr6:25115527-25115528
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25110740..25112750-chr6:25114092..25116124,2	K562	blood:
2	chr6:25112288..25113816-chr6:25114376..25117367,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1002596	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1547054	0.81[ASN][1000 genomes]
rs1547055	0.81[ASN][1000 genomes]
rs159988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs167329	0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16890104	0.88[JPT][hapmap]
rs2028973	0.88[JPT][hapmap]
rs2166682	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394363	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302966	0.89[JPT][hapmap]
rs302973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs302976	0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302980	0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs302982	0.87[ASN][1000 genomes]
rs302983	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs302990	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs302991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs303000	0.86[CHB][hapmap]
rs303006	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303007	0.89[JPT][hapmap]
rs303008	0.89[JPT][hapmap]
rs303009	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303015	0.84[JPT][hapmap]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.88[JPT][hapmap]
rs3792970	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792986	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818268	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs392852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs456816	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4711077	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711078	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906102	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715426	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715427	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7740661	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs7740668	0.89[CEU][hapmap]
rs9295646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9356961	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9358833	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379717	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379719	0.89[ASN][1000 genomes]
rs9393613	0.88[CHB][hapmap]
rs9393617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9654585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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
rs2166683	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs2166683	CMAH	cis	multi-tissue	Pritchard
rs2166683	CMAHP	cis	Artery Tibial	GTEx
rs2166683	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
2	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
4	chr6:25096000-25116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25099000-25116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:25099000-25117400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:25101400-25115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:25102000-25116200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:25102800-25117600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:25103200-25116000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr6:25103200-25116000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:25103400-25116000	Strong transcription	Primary T cells from cord blood	blood
14	chr6:25103600-25116000	Strong transcription	HSMMtube	muscle
15	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
16	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:25105200-25116000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:25105600-25115600	Weak transcription	Pancreas	Pancrea
19	chr6:25105600-25116000	Strong transcription	Placenta	Placenta
20	chr6:25106000-25115600	Weak transcription	Right Ventricle	heart
21	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:25108600-25116000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:25108800-25116400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
27	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
31	chr6:25111000-25116000	Strong transcription	Primary B cells from cord blood	blood
32	chr6:25112400-25115800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:25112600-25115800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:25112800-25116000	Strong transcription	Lung	lung
35	chr6:25112800-25116600	Weak transcription	Fetal Stomach	stomach
36	chr6:25113000-25136800	Weak transcription	Osteobl	bone
37	chr6:25113200-25116000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:25113400-25115800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr6:25113400-25124200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:25113600-25116000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:25113600-25116000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:25113800-25115800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr6:25113800-25121200	Genic enhancers	Dnd41	blood
45	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
46	chr6:25114200-25115800	Weak transcription	Gastric	stomach
47	chr6:25114200-25122200	Weak transcription	HSMM	muscle
48	chr6:25114600-25122200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:25114600-25125800	Weak transcription	GM12878-XiMat	blood
50	chr6:25114800-25115800	Strong transcription	Fetal Thymus	thymus

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