Variant report

Variant	rs2515186
Chromosome Location	chr8:104139855-104139856
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	chr8:104135020..104140740-chr8:104310050..104312668,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247081	Chromatin interaction
ENSG00000164930	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1113126	0.85[ASN][1000 genomes]
rs1497449	0.80[ASN][1000 genomes]
rs1497450	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1497451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1497452	1.00[ASN][1000 genomes]
rs1846063	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1846064	1.00[ASN][1000 genomes]
rs1976326	0.92[ASN][1000 genomes]
rs2132867	0.92[ASN][1000 genomes]
rs2249240	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2249254	0.83[ASN][1000 genomes]
rs2249255	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2249256	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs2256164	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454000	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454001	0.92[ASN][1000 genomes]
rs2454002	0.92[ASN][1000 genomes]
rs2454003	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2454004	0.92[ASN][1000 genomes]
rs2454005	0.85[ASN][1000 genomes]
rs2454006	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2454013	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454014	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2454032	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2454033	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2454036	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2454037	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2454038	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2515175	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2515176	0.85[ASN][1000 genomes]
rs2515178	0.85[ASN][1000 genomes]
rs2515181	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs2515182	0.89[ASN][1000 genomes]
rs2515184	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2515190	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2935579	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2935593	0.85[ASN][1000 genomes]
rs3019158	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3019159	0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs4734071	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4734687	0.86[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs4734689	0.80[ASN][1000 genomes]
rs4734690	0.80[ASN][1000 genomes]
rs7001897	0.80[ASN][1000 genomes]
rs953253	0.91[ASN][1000 genomes]
rs991312	0.91[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2515186	BAALC	cis	parietal	SCAN
rs2515186	BAALC	cis	cerebellum	SCAN
rs2515186	SLC25A32	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104134400-104145000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:104136000-104143200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:104137600-104142800	Weak transcription	NHDF-Ad	bronchial
4	chr8:104137800-104143600	Weak transcription	Brain Anterior Caudate	brain
5	chr8:104138000-104141600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr8:104138000-104143800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:104139200-104140600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:104139400-104140000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr8:104139400-104140200	Enhancers	Osteobl	bone
10	chr8:104139400-104140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr8:104139600-104140000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:104139600-104140600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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