Variant report

Variant	rs12548629
Chromosome Location	chr8:104201401-104201402
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	chr4:148610239..148613051-chr8:104200135..104201752,2	MCF-7	breast:
2	chr8:104201251..104203318-chr8:104203773..104206648,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11784151	0.89[AFR][1000 genomes]
rs12541167	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs12543038	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs13275173	0.89[AFR][1000 genomes]
rs13279226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1353212	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1353213	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1522707	0.84[ASW][hapmap]
rs16870243	0.93[ASN][1000 genomes]
rs16870245	0.93[ASN][1000 genomes]
rs16870249	0.93[ASN][1000 genomes]
rs16870261	0.82[YRI][hapmap]
rs17204757	0.85[AFR][1000 genomes]
rs17205332	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17799604	0.81[ASN][1000 genomes]
rs2220825	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3107646	0.84[ASW][hapmap]
rs34185273	0.87[ASN][1000 genomes]
rs34337822	0.93[ASN][1000 genomes]
rs4734693	0.81[ASN][1000 genomes]
rs7002269	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9656787	0.84[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv14660	chr8:104182119-104245529	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12548629	FZD6	cis	cerebellum	SCAN
rs12548629	KLF10	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104192800-104219200	Weak transcription	Aorta	Aorta
2	chr8:104193000-104204800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr8:104193000-104209000	Weak transcription	Brain Substantia Nigra	brain
4	chr8:104193400-104220000	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:104193600-104201800	Weak transcription	Spleen	Spleen
6	chr8:104193600-104220200	Weak transcription	Brain Anterior Caudate	brain
7	chr8:104194200-104217600	Weak transcription	Fetal Brain Female	brain
8	chr8:104196600-104201800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:104197000-104210000	Weak transcription	Brain Angular Gyrus	brain
10	chr8:104197200-104218600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr8:104198200-104201800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:104198600-104202800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:104198600-104204200	Weak transcription	HSMMtube	muscle
14	chr8:104198600-104210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr8:104199600-104202200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr8:104199800-104208800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:104200000-104204400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:104200000-104204800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:104200000-104215000	Weak transcription	NHDF-Ad	bronchial
20	chr8:104200200-104201800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr8:104200200-104201800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr8:104200200-104204600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:104200600-104205400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:104200800-104201600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:104201200-104201600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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