Variant report

Variant	rs2504048
Chromosome Location	chr1:179722827-179722828
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179715653..179718045-chr1:179722223..179724406,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1052447	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10798718	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10798719	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs10798720	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs10798721	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10913874	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10913875	0.90[CHB][hapmap]
rs10913876	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10913877	0.85[ASN][1000 genomes]
rs10913878	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs10913879	0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs11578918	0.90[CHB][hapmap]
rs11588754	0.95[ASN][1000 genomes]
rs12047821	0.84[ASN][1000 genomes]
rs12408874	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs12408882	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs16854629	0.90[CHB][hapmap]
rs2245195	0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs2245610	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318389	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2454195	0.85[ASN][1000 genomes]
rs2454196	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2454197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487739	0.88[ASN][1000 genomes]
rs2487740	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2487746	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2504032	0.93[ASN][1000 genomes]
rs2504033	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2504034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs2504035	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504038	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504039	0.85[ASN][1000 genomes]
rs2504040	0.85[ASN][1000 genomes]
rs2504041	0.85[ASN][1000 genomes]
rs2504042	0.85[ASN][1000 genomes]
rs2504043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504053	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs3845381	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3845382	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs3845383	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs3856045	0.85[ASN][1000 genomes]
rs3909014	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs3909015	0.85[ASN][1000 genomes]
rs4469684	0.85[ASN][1000 genomes]
rs4511077	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4651050	0.82[ASN][1000 genomes]
rs60556788	0.83[ASN][1000 genomes]
rs61828370	0.84[ASN][1000 genomes]
rs6663482	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548339	chr1:179686244-179722827	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2504048	CEP350	cis	cerebellum	SCAN
rs2504048	IER5	cis	parietal	SCAN
rs2504048	TNR	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179721600-179723800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:179722400-179723800	Enhancers	Osteobl	bone
3	chr1:179722400-179724000	Enhancers	Colon Smooth Muscle	Colon
4	chr1:179722600-179724000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:179722600-179724000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:179722800-179723600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:179722800-179723800	Enhancers	HSMMtube	muscle
8	chr1:179722800-179724000	Enhancers	Rectal Smooth Muscle	rectum

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