Variant report

Variant	rs4734687
Chromosome Location	chr8:104131722-104131723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr8:104131618-104131955	MCF10A-Er-Src	breast:	n/a	chr8:104131786-104131797 chr8:104131787-104131795
2	FOS	chr8:104131653-104131854	MCF10A-Er-Src	breast:	n/a	chr8:104131786-104131797 chr8:104131787-104131795
3	FOS	chr8:104131617-104131954	MCF10A-Er-Src	breast:	n/a	chr8:104131786-104131797 chr8:104131787-104131795

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104130679..104132364-chr8:104143004..104144519,2	MCF-7	breast:
2	chr8:104131678..104134497-chr8:104225293..104227549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250929	TF binding region
ENSG00000164929	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	0.88[ASN][1000 genomes]
rs1497449	0.82[ASN][1000 genomes]
rs1497450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1497451	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1497452	0.85[ASN][1000 genomes]
rs1846063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1846064	0.85[ASN][1000 genomes]
rs1976326	0.93[ASN][1000 genomes]
rs2132867	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2249240	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249254	0.85[ASN][1000 genomes]
rs2249255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2249256	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256164	0.91[JPT][hapmap]
rs2454000	0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.85[ASN][1000 genomes]
rs2454001	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454002	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454004	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2454005	0.87[ASN][1000 genomes]
rs2454006	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454013	0.91[JPT][hapmap]
rs2454014	0.91[JPT][hapmap]
rs2454032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515176	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2515178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2515182	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2515184	0.85[ASN][1000 genomes]
rs2515185	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2515186	0.86[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs2515190	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2935579	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2935593	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019158	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];1.00[ASN][1000 genomes]
rs3019159	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4734071	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4734689	0.82[ASN][1000 genomes]
rs4734690	0.82[ASN][1000 genomes]
rs7001897	0.82[ASN][1000 genomes]
rs953253	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs991312	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[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
rs4734687	SLC25A32	cis	cerebellum	SCAN
rs4734687	BAALC	cis	parietal	SCAN
rs4734687	BAALC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104119400-104134000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:104122000-104134600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:104123600-104132600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:104126600-104132000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:104127200-104132000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:104127400-104133200	Weak transcription	HSMMtube	muscle
7	chr8:104128400-104132800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:104128600-104132600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr8:104128600-104133000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr8:104128800-104132000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:104128800-104132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:104128800-104132400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr8:104128800-104132400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:104128800-104132600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:104128800-104132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr8:104128800-104133200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:104128800-104134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:104129000-104131800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:104129000-104133400	Weak transcription	Osteobl	bone
20	chr8:104129800-104131800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:104130800-104133000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr8:104131000-104132200	Enhancers	NHEK	skin
23	chr8:104131000-104132800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr8:104131000-104135200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:104131200-104132200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr8:104131200-104132400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr8:104131200-104132600	Enhancers	NH-A	brain
28	chr8:104131200-104134000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr8:104131200-104134000	Enhancers	HMEC	breast
30	chr8:104131200-104136400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:104131400-104132200	Weak transcription	NHDF-Ad	bronchial
32	chr8:104131600-104132600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr8:104131600-104133400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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