Variant report

Variant	rs9295647
Chromosome Location	chr6:25093433-25093434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1002596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159988	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs167329	0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs16890104	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs1923195	0.89[CHD][hapmap];0.86[MEX][hapmap]
rs2028973	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs2166682	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2166683	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]
rs2394363	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894033	0.89[CHD][hapmap];0.86[MEX][hapmap]
rs302966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs302973	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs302976	0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs302980	0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs302983	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs302987	0.82[ASN][1000 genomes]
rs302989	0.84[CHD][hapmap]
rs302990	0.83[CHD][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs302991	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs303000	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs303004	0.90[ASN][1000 genomes]
rs303006	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303009	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs303015	0.84[JPT][hapmap]
rs303016	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs303018	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs303026	0.88[ASW][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap]
rs3792970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792971	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812105	0.88[CHD][hapmap]
rs3818268	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391626	0.90[ASN][1000 genomes]
rs392852	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs398672	0.90[ASN][1000 genomes]
rs420369	0.90[ASN][1000 genomes]
rs456816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711077	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712887	0.89[CHD][hapmap]
rs6906102	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]
rs715426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715427	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740661	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7740668	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs7775959	0.83[ASN][1000 genomes]
rs7776121	0.83[ASN][1000 genomes]
rs9295646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356961	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358833	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379717	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393613	0.86[CHB][hapmap]
rs9393617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9654585	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9295647	BTN2A1	cis	cerebellum	SCAN
rs9295647	LTBP4	trans	parietal	SCAN
rs9295647	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs9295647	CMAH	cis	cerebellum	SCAN
rs9295647	CMAH	cis	lymphoblastoid	seeQTL
rs9295647	CMAH	cis	parietal	SCAN
rs9295647	CMAH	cis	multi-tissue	Pritchard
rs9295647	HIST1H2BM	cis	cerebellum	SCAN
rs9295647	LRRC16A	cis	parietal	SCAN
rs9295647	HIST1H2AK	cis	parietal	SCAN
rs9295647	CMAHP	cis	Thyroid	GTEx
rs9295647	CMAHP	cis	Artery Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:25084800-25113800	Weak transcription	Gastric	stomach
6	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
8	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
9	chr6:25086600-25096600	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
11	chr6:25087400-25098200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
14	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
16	chr6:25087800-25097200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:25088400-25096600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:25088400-25105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:25088400-25113800	Strong transcription	Dnd41	blood
21	chr6:25088600-25098000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:25089200-25095000	Weak transcription	Spleen	Spleen
23	chr6:25089200-25106000	Weak transcription	Osteobl	bone
24	chr6:25089200-25108400	Weak transcription	HSMM	muscle
25	chr6:25089800-25103600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:25090000-25098200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:25090000-25098400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:25090200-25094800	Weak transcription	HUVEC	blood vessel
29	chr6:25090200-25095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:25090200-25097600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:25090400-25095000	Weak transcription	Aorta	Aorta
32	chr6:25090400-25103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:25090400-25105400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:25091200-25093600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:25091200-25094200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25091400-25093800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr6:25091400-25094200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr6:25091400-25097600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:25091600-25103600	Weak transcription	HSMMtube	muscle
40	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:25091800-25103600	Weak transcription	Psoas Muscle	Psoas
42	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
43	chr6:25092200-25095200	Weak transcription	Liver	Liver
44	chr6:25092800-25098000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr6:25093000-25093600	Enhancers	NHEK	skin
46	chr6:25093000-25094000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:25093000-25094000	Strong transcription	Ovary	ovary
48	chr6:25093000-25094800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:25093000-25096000	Strong transcription	Primary T cells from cord blood	blood
50	chr6:25093000-25096400	Strong transcription	Primary B cells from peripheral blood	blood

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