Variant report

Variant	rs1547054
Chromosome Location	chr6:25111089-25111090
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25110856..25114923-chr6:25121965..25124614,3	MCF-7	breast:
2	chr6:25110740..25112750-chr6:25114092..25116124,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1547055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823184	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1838967	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1923195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2145769	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166683	0.81[ASN][1000 genomes]
rs2295737	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2516577	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2894033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs302967	1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs302968	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs302969	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs302970	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs302977	0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs302978	0.82[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs302979	1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs302984	1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs302989	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs303022	1.00[JPT][hapmap]
rs303025	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3812105	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818267	0.86[YRI][hapmap]
rs3818270	0.86[YRI][hapmap]
rs4712887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6919920	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935318	0.85[YRI][hapmap]
rs7739547	0.87[YRI][hapmap]
rs7740661	0.84[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7740668	0.85[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773802	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7775959	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7776121	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9379721	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9393613	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393615	0.85[EUR][1000 genomes]
rs9393616	0.98[EUR][1000 genomes];0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1547054	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs1547054	CMAHP	cis	Thyroid	GTEx
rs1547054	CMAH	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25084800-25113800	Weak transcription	Gastric	stomach
2	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
3	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
4	chr6:25088400-25113800	Strong transcription	Dnd41	blood
5	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
7	chr6:25096000-25116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:25099000-25116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:25099000-25117400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:25100800-25112200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25101400-25115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:25102000-25116200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:25102800-25117600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:25103200-25116000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr6:25103200-25116000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:25103400-25116000	Strong transcription	Primary T cells from cord blood	blood
18	chr6:25103600-25116000	Strong transcription	HSMMtube	muscle
19	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
20	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:25105000-25112200	Weak transcription	Fetal Lung	lung
22	chr6:25105200-25116000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:25105600-25112400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:25105600-25115600	Weak transcription	Pancreas	Pancrea
25	chr6:25105600-25116000	Strong transcription	Placenta	Placenta
26	chr6:25105800-25115000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr6:25105800-25115000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:25106000-25115600	Weak transcription	Right Ventricle	heart
29	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
30	chr6:25106400-25112600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:25106600-25112400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:25108200-25112400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:25108200-25112400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:25108600-25111600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr6:25108600-25113200	Weak transcription	Spleen	Spleen
38	chr6:25108600-25116000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:25108800-25112800	Weak transcription	Lung	lung
40	chr6:25108800-25113200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:25108800-25113600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:25108800-25113800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:25108800-25116400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
45	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:25109000-25113800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:25109000-25113800	Weak transcription	HSMM	muscle
48	chr6:25109400-25112000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:25109600-25114600	Strong transcription	GM12878-XiMat	blood
50	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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