Variant report

Variant	rs12550247
Chromosome Location	chr8:125193556-125193557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125191098..125195627-chr8:125383123..125386679,7	MCF-7	breast:
2	chr8:125052777..125055387-chr8:125192155..125193745,2	MCF-7	breast:
3	chr8:125148790..125152078-chr8:125191101..125194599,4	MCF-7	breast:
4	chr8:125192128..125194093-chr8:125383543..125386541,2	MCF-7	breast:
5	chr8:125192130..125196319-chr8:125210764..125213937,4	MCF-7	breast:
6	chr8:125191744..125194449-chr8:125391340..125393349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181171	Chromatin interaction
ENSG00000164983	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10091262	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10091270	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114156	0.92[ASN][1000 genomes]
rs12545670	0.80[CHB][hapmap]
rs12680268	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4242360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6470227	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6470230	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986229	0.85[CHB][hapmap];0.86[GIH][hapmap]
rs6991843	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6991906	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015364	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7817281	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv612144	chr8:125057728-125206503	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1023183	chr8:125060532-125206445	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv948556	chr8:125067187-125204721	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv831452	chr8:125099708-125259926	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv891429	chr8:125163219-125246937	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12550247	FAM83A	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125184200-125193600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:125184400-125193600	Weak transcription	K562	blood
3	chr8:125184400-125195600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:125190000-125198600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:125191200-125196800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr8:125192000-125196000	Enhancers	NHDF-Ad	bronchial
7	chr8:125192200-125194000	Enhancers	Osteobl	bone
8	chr8:125192200-125194400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr8:125192200-125194400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr8:125192200-125194600	Enhancers	Fetal Muscle Leg	muscle
11	chr8:125192200-125195400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:125192400-125194000	Enhancers	Fetal Kidney	kidney
13	chr8:125192400-125194400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:125192400-125194400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:125192600-125193600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:125192600-125194400	Enhancers	Fetal Lung	lung
17	chr8:125192600-125194600	Enhancers	Psoas Muscle	Psoas
18	chr8:125192600-125194600	Enhancers	HSMMtube	muscle
19	chr8:125192600-125196000	Enhancers	Hela-S3	cervix
20	chr8:125192600-125196000	Enhancers	NHLF	lung
21	chr8:125193000-125196000	Enhancers	NH-A	brain
22	chr8:125193200-125193600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:125193200-125194000	Enhancers	Fetal Thymus	thymus
24	chr8:125193200-125194200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:125193200-125194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:125193200-125194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:125193200-125194600	Enhancers	HUVEC	blood vessel
28	chr8:125193200-125196000	Enhancers	HSMM	muscle
29	chr8:125193400-125193600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr8:125193400-125193600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr8:125193400-125194400	Enhancers	Primary hematopoietic stem cells	blood
32	chr8:125193400-125194400	Enhancers	NHEK	skin

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