Variant report

Variant	rs6906102
Chromosome Location	chr6:25090257-25090258
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	chr6:25085087..25087243-chr6:25089273..25091853,2	K562	blood:

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

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

rs_ID	r²[population]
rs1002596	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16890104	0.88[JPT][hapmap]
rs2028973	0.88[JPT][hapmap]
rs2166682	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2166683	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]
rs2394363	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs302966	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs302973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs302976	0.83[ASN][1000 genomes]
rs302980	0.83[ASN][1000 genomes]
rs302983	0.88[JPT][hapmap]
rs302987	0.82[ASN][1000 genomes]
rs302991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303000	0.86[CHB][hapmap]
rs303004	0.90[ASN][1000 genomes]
rs303006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303007	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303008	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.88[JPT][hapmap]
rs3792970	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792971	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792986	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391626	0.90[ASN][1000 genomes]
rs392852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs398672	0.90[ASN][1000 genomes]
rs420369	0.90[ASN][1000 genomes]
rs456816	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711077	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711078	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs715426	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715427	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740661	0.88[CHB][hapmap]
rs7740668	0.89[CHB][hapmap]
rs7775959	0.83[ASN][1000 genomes]
rs7776121	0.83[ASN][1000 genomes]
rs9295646	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295647	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356961	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358833	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379717	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393613	0.88[CHB][hapmap]
rs9393617	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9654585	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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
rs6906102	CMAH	cis	multi-tissue	Pritchard
rs6906102	CMAHP	cis	Artery Tibial	GTEx
rs6906102	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs6906102	CMAHP	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25079400-25093000	Weak transcription	Ovary	ovary
2	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
7	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
8	chr6:25084800-25113800	Weak transcription	Gastric	stomach
9	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
12	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
13	chr6:25086600-25090400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr6:25087000-25090600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:25087000-25093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
18	chr6:25087200-25091400	Weak transcription	Esophagus	oesophagus
19	chr6:25087400-25092200	Weak transcription	Primary B cells from cord blood	blood
20	chr6:25087400-25098200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
23	chr6:25087600-25091200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
26	chr6:25087800-25093000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:25087800-25093400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:25087800-25097200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:25088200-25091200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:25088400-25090400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr6:25088400-25096600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:25088400-25105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:25088400-25113800	Strong transcription	Dnd41	blood
35	chr6:25088600-25090400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25088600-25090400	Enhancers	HMEC	breast
37	chr6:25088600-25090400	Enhancers	NHEK	skin
38	chr6:25088600-25090600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr6:25088600-25090800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:25088600-25098000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:25088800-25091200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:25089000-25090400	Strong transcription	Aorta	Aorta
43	chr6:25089200-25095000	Weak transcription	Spleen	Spleen
44	chr6:25089200-25106000	Weak transcription	Osteobl	bone
45	chr6:25089200-25108400	Weak transcription	HSMM	muscle
46	chr6:25089400-25091400	Weak transcription	HSMMtube	muscle
47	chr6:25089600-25090400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:25089600-25091600	Weak transcription	Adipose Nuclei	Adipose
49	chr6:25089600-25093000	Weak transcription	Lung	lung
50	chr6:25089800-25090400	Enhancers	Primary neutrophils fromperipheralblood	blood

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