Variant report

Variant	rs4148666
Chromosome Location	chr12:22031991-22031992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:22031693..22034334-chr13:31039008..31041172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189403	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10841902	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11046212	0.88[CHB][hapmap]
rs11046215	0.82[CHB][hapmap]
rs1283808	0.87[ASN][1000 genomes]
rs1388698	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1492137	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1914361	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs1965033	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2032775	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2292771	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2307024	0.82[CHB][hapmap]
rs3782668	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4148661	0.87[ASN][1000 genomes]
rs4148669	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4762717	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs704185	0.82[CHB][hapmap]
rs704191	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs704192	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs7314764	0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7978092	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

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	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv470275	chr12:21938544-22126314	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1847099	chr12:22003544-22035425	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv898899	chr12:22024093-22044210	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4148666	ABCC9	cis	parietal	SCAN
rs4148666	RERGL	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21995600-22034800	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:22014800-22034800	Weak transcription	Ovary	ovary
3	chr12:22023600-22034800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:22024400-22034800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:22024800-22037000	Weak transcription	Left Ventricle	heart
6	chr12:22024800-22044000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:22024800-22044800	Weak transcription	Aorta	Aorta
8	chr12:22025000-22033600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:22025800-22034600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:22027000-22034600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:22027000-22041000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:22027600-22046200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:22029400-22040800	Weak transcription	Fetal Lung	lung
14	chr12:22030000-22032800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:22030600-22044800	Weak transcription	Right Ventricle	heart
16	chr12:22030800-22034600	Weak transcription	Psoas Muscle	Psoas
17	chr12:22031200-22032000	Flanking Active TSS	Fetal Heart	heart
18	chr12:22031200-22032800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:22031400-22032200	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:22031600-22039400	Enhancers	Liver	Liver
21	chr12:22031800-22034800	Weak transcription	Adipose Nuclei	Adipose

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