Variant report

Variant	rs12566823
Chromosome Location	chr1:171158284-171158285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171049785..171051089-chr1:171157506..171158409,9	MCF-7	breast:
2	chr1:170936285..170936841-chr1:171157519..171158468,2	MCF-7	breast:
3	chr1:171151483..171154581-chr1:171157949..171161924,3	MCF-7	breast:
4	chr1:171157094..171159925-chr1:171161242..171162761,2	K562	blood:
5	chr1:171050091..171050825-chr1:171157560..171158443,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094963	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10798253	0.81[ASN][1000 genomes]
rs10798263	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10798271	0.81[GIH][hapmap]
rs10912537	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10912538	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10912542	0.80[ASN][1000 genomes]
rs10912552	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10912593	0.81[GIH][hapmap]
rs11806072	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs11810116	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12078953	0.95[JPT][hapmap]
rs12080576	0.93[JPT][hapmap]
rs12085225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12092242	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12567059	0.95[ASN][1000 genomes]
rs12567358	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12567600	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12758140	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17350523	0.95[JPT][hapmap]
rs2020862	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap]
rs2064078	0.95[JPT][hapmap]
rs2075987	0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2075990	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2075991	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2179105	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2205723	0.80[ASN][1000 genomes]
rs2205724	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2205729	0.95[JPT][hapmap]
rs2236874	0.95[JPT][hapmap]
rs28369823	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28369838	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28369839	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28369841	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28369847	0.98[ASN][1000 genomes]
rs3738813	0.95[JPT][hapmap]
rs3754495	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768569	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768570	0.95[JPT][hapmap]
rs4916182	0.80[ASN][1000 genomes]
rs6425394	0.95[JPT][hapmap]
rs6657314	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs6662773	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6692260	0.80[ASN][1000 genomes]
rs6692347	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6699803	0.80[ASN][1000 genomes]
rs7513579	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7518899	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7531971	0.95[JPT][hapmap]
rs7534749	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539549	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7540349	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550060	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7555557	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs926268	0.95[JPT][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12566823	FMO2	cis	cerebellum	SCAN
rs12566823	TNFSF18	cis	cerebellum	SCAN
rs12566823	FMO2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171153400-171159000	Active TSS	Aorta	Aorta
2	chr1:171154000-171159600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:171154200-171158800	Active TSS	Psoas Muscle	Psoas
4	chr1:171154200-171159000	Active TSS	Left Ventricle	heart
5	chr1:171154200-171160800	Active TSS	Right Atrium	heart
6	chr1:171156000-171158400	Enhancers	Fetal Lung	lung
7	chr1:171156400-171165800	Weak transcription	Gastric	stomach
8	chr1:171156600-171158600	Weak transcription	Lung	lung
9	chr1:171156600-171163800	Weak transcription	Small Intestine	intestine
10	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
12	chr1:171156600-171179600	Weak transcription	NHLF	lung
13	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
14	chr1:171157200-171158400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:171157400-171159000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr1:171157600-171160000	Enhancers	Fetal Intestine Large	intestine
17	chr1:171157800-171165600	Weak transcription	Ovary	ovary
18	chr1:171158000-171158400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:171158000-171158400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:171158000-171158400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:171158000-171158400	Active TSS	Liver	Liver
22	chr1:171158000-171160000	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:171158200-171158400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:171158200-171158400	Enhancers	NHEK	skin
25	chr1:171158200-171160000	Enhancers	Fetal Intestine Small	intestine
26	chr1:171158200-171167000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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