Variant report

Variant	rs827541
Chromosome Location	chr8:104292965-104292966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104288724..104293754-chr8:104308710..104311344,7	MCF-7	breast:
2	chr8:104290643..104293920-chr8:104294034..104295976,4	MCF-7	breast:
3	chr8:104289531..104293502-chr8:104385386..104388063,3	MCF-7	breast:
4	chr8:104291913..104293426-chr8:104426579..104428260,2	MCF-7	breast:
5	chr8:104290229..104295041-chr8:104295678..104299330,4	MCF-7	breast:
6	chr8:104292150..104293871-chr8:104425235..104426887,2	MCF-7	breast:
7	chr8:104290160..104293505-chr8:104310027..104313255,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164930	Chromatin interaction
ENSG00000247081	Chromatin interaction
ENSG00000164933	Chromatin interaction
ENSG00000164934	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004468	0.81[CEU][hapmap]
rs10096928	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10505042	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1053917	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs1095713	0.84[GIH][hapmap]
rs1095714	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1157213	0.80[MEX][hapmap];0.87[TSI][hapmap]
rs11781252	0.80[CEU][hapmap]
rs12546491	0.80[CEU][hapmap]
rs12550097	0.81[EUR][1000 genomes]
rs13277869	0.80[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs1494280	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1522707	0.83[JPT][hapmap]
rs1522708	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1522710	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1522711	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1522712	0.82[EUR][1000 genomes]
rs16870346	0.80[CEU][hapmap]
rs1851483	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2642363	0.83[EUR][1000 genomes]
rs2642364	0.83[EUR][1000 genomes]
rs2642366	0.83[EUR][1000 genomes]
rs2642368	0.85[EUR][1000 genomes]
rs28392906	0.82[EUR][1000 genomes]
rs2934726	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3104033	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3107646	0.83[JPT][hapmap]
rs3133798	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133833	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3133837	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35935697	0.81[EUR][1000 genomes]
rs3736047	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3808553	0.81[CEU][hapmap];0.87[GIH][hapmap];0.80[EUR][1000 genomes]
rs3808554	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs3808556	0.81[EUR][1000 genomes]
rs3808559	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs62525511	0.81[EUR][1000 genomes]
rs6999018	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827535	0.84[GIH][hapmap]
rs827536	0.84[GIH][hapmap]
rs827581	0.82[GIH][hapmap]
rs827584	0.85[GIH][hapmap]
rs827585	0.85[GIH][hapmap]
rs827588	0.82[GIH][hapmap]

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	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs827541	SLC25A32	cis	cerebellum	SCAN
rs827541	GRHL2	cis	cerebellum	SCAN
rs827541	FZD6	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104284800-104295400	Weak transcription	Aorta	Aorta
2	chr8:104288400-104295400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:104288600-104293200	Weak transcription	NH-A	brain
4	chr8:104288800-104293400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:104289200-104302000	Weak transcription	Fetal Heart	heart
6	chr8:104290200-104293600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:104290200-104293800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:104290600-104293400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:104291200-104293600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:104291200-104294000	Enhancers	Primary hematopoietic stem cells	blood
11	chr8:104291200-104294200	Enhancers	HUVEC	blood vessel
12	chr8:104291400-104294000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr8:104291400-104294800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr8:104291800-104293400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:104291800-104293400	Weak transcription	NHLF	lung
16	chr8:104291800-104293800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr8:104292000-104293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:104292000-104293200	Weak transcription	NHDF-Ad	bronchial
19	chr8:104292000-104293400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr8:104292000-104293400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr8:104292000-104293800	Weak transcription	Fetal Stomach	stomach
22	chr8:104292000-104293800	Weak transcription	Left Ventricle	heart
23	chr8:104292200-104293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:104292200-104293200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:104292200-104293200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr8:104292400-104293400	Weak transcription	Adipose Nuclei	Adipose
27	chr8:104292400-104294000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:104292600-104293000	Weak transcription	Osteobl	bone
29	chr8:104292800-104295400	Enhancers	HepG2	liver

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