Variant report

Variant	rs12035144
Chromosome Location	chr1:169749154-169749155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169680922..169681530-chr1:169748582..169749325,2	MCF-7	breast:
2	chr1:169742421..169744190-chr1:169747742..169750405,2	MCF-7	breast:
3	chr1:169747522..169750361-chr1:169754241..169756814,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10157246	0.95[AMR][1000 genomes];0.99[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];0.98[AMR][1000 genomes];0.99[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];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10800476	0.81[MEX][hapmap]
rs10919236	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919237	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919240	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919242	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919243	0.89[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11588275	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129417	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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404614	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205845	0.82[MEX][hapmap]
rs2420507	0.84[AMR][1000 genomes];0.94[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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676623	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676718	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683782	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696884	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6701718	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722511	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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
rs12035144	C1orf112	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169745200-169749200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:169748200-169749400	Enhancers	Liver	Liver
3	chr1:169748200-169749600	Enhancers	HepG2	liver
4	chr1:169748200-169753600	Enhancers	HUVEC	blood vessel
5	chr1:169748400-169751000	Enhancers	Osteobl	bone
6	chr1:169748400-169751400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:169748800-169749600	Enhancers	NH-A	brain
8	chr1:169748800-169750200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:169748800-169750400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:169748800-169750600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:169748800-169751000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:169749000-169749200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:169749000-169749400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:169749000-169749600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169749000-169749600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:169749000-169749600	Flanking Active TSS	A549	lung
17	chr1:169749000-169750200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:169749000-169750200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:169749000-169750200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:169749000-169750400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:169749000-169750400	Enhancers	HMEC	breast
22	chr1:169749000-169750800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:169749000-169750800	Enhancers	NHLF	lung
24	chr1:169749000-169751400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:169749000-169751600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:169749000-169751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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