Variant report

Variant	rs12129417
Chromosome Location	chr1:169750529-169750530
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169749828..169751935-chr1:169761996..169767099,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157246	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10157266	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10157398	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs10753794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753795	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10753796	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10800476	0.81[MEX][hapmap]
rs10919236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919237	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919243	0.89[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11588275	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035144	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404614	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205845	0.82[MEX][hapmap]
rs2420507	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753311	0.84[CEU][hapmap]
rs6427216	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6427219	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676718	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683782	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696884	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6701718	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549412	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12129417	C1orf112	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169748200-169753600	Enhancers	HUVEC	blood vessel
2	chr1:169748400-169751000	Enhancers	Osteobl	bone
3	chr1:169748400-169751400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:169748800-169750600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:169748800-169751000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:169749000-169750800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:169749000-169750800	Enhancers	NHLF	lung
8	chr1:169749000-169751400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:169749000-169751600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:169749000-169751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:169749400-169750600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:169749400-169750600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:169749400-169750600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:169749400-169750800	Enhancers	Hela-S3	cervix
15	chr1:169749400-169752000	Enhancers	NHEK	skin
16	chr1:169749400-169761400	Weak transcription	Liver	Liver
17	chr1:169749600-169750600	Weak transcription	NH-A	brain
18	chr1:169749600-169751000	Enhancers	A549	lung
19	chr1:169750000-169750600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:169750000-169750600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:169750000-169750800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:169750000-169752400	Enhancers	Placenta	Placenta
23	chr1:169750200-169750800	Enhancers	K562	blood
24	chr1:169750200-169751000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:169750200-169751200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:169750200-169753000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:169750400-169750600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:169750400-169750800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:169750400-169750800	Active TSS	HMEC	breast
30	chr1:169750400-169751000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:169750400-169751000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:169750400-169754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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