Variant report

Variant	rs9295646
Chromosome Location	chr6:25078882-25078883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25077616..25079244-chr6:25083484..25086101,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168405	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159988	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs16890104	0.88[CHD][hapmap]
rs1923195	0.85[CHD][hapmap]
rs2028973	0.84[CHD][hapmap]
rs2166682	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2166683	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]
rs2394363	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894033	0.85[CHD][hapmap]
rs302966	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs302973	1.00[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs302976	0.83[ASN][1000 genomes]
rs302980	0.83[ASN][1000 genomes]
rs302983	0.81[CHD][hapmap]
rs302987	0.82[ASN][1000 genomes]
rs302989	0.81[CHD][hapmap]
rs302991	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs303000	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs303004	0.90[ASN][1000 genomes]
rs303006	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs303007	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs303008	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs303009	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs303016	0.80[CHD][hapmap]
rs303018	0.80[CHD][hapmap]
rs303026	0.84[CHD][hapmap]
rs3792970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792971	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];0.96[ASN][1000 genomes]
rs3792986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812105	0.84[CHD][hapmap]
rs3818268	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391626	0.90[ASN][1000 genomes]
rs392852	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[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];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711077	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711078	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712887	0.85[CHD][hapmap]
rs6906102	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]
rs715426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715427	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740661	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs7740668	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs7775959	0.83[ASN][1000 genomes]
rs7776121	0.83[ASN][1000 genomes]
rs9295647	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358833	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379717	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393613	0.86[CHB][hapmap]
rs9393617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9654585	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9295646	LTBP4	trans	parietal	SCAN
rs9295646	CMAH	cis	parietal	SCAN
rs9295646	CMAH	cis	multi-tissue	Pritchard
rs9295646	CMAH	cis	lymphoblastoid	seeQTL
rs9295646	HIST1H2AK	cis	parietal	SCAN
rs9295646	CMAH	cis	cerebellum	SCAN
rs9295646	CMAHP	cis	Thyroid	GTEx
rs9295646	BTN2A1	cis	cerebellum	SCAN
rs9295646	CMAH	cis	normal skin	skin_eQTL
rs9295646	HIST1H2BM	cis	cerebellum	SCAN
rs9295646	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs9295646	CMAHP	cis	Artery Tibial	GTEx
rs9295646	LRRC16A	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25057600-25080400	Weak transcription	Thymus	Thymus
2	chr6:25063200-25079200	Weak transcription	Ovary	ovary
3	chr6:25067400-25080400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:25067600-25084600	Weak transcription	HSMMtube	muscle
5	chr6:25069800-25084000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:25071000-25080400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:25071000-25084400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:25071200-25080000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:25071200-25080200	Weak transcription	Dnd41	blood
10	chr6:25071200-25080400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:25071200-25080800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:25071200-25080800	Weak transcription	Fetal Thymus	thymus
13	chr6:25071200-25082000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:25071200-25082400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:25071200-25082600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:25071200-25083800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:25071200-25083800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:25071200-25084000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:25071200-25084000	Weak transcription	Placenta	Placenta
20	chr6:25071200-25084000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:25071200-25084600	Weak transcription	Adipose Nuclei	Adipose
22	chr6:25071200-25085200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:25071200-25085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:25071400-25084800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:25071400-25085600	Weak transcription	Primary B cells from cord blood	blood
26	chr6:25072200-25080600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:25075600-25080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:25075800-25080600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:25075800-25080600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:25075800-25080600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25076200-25084200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:25077000-25086600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:25078400-25080600	Weak transcription	Left Ventricle	heart

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