Variant report

Variant	rs398444
Chromosome Location	chr20:31649781-31649782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:31648171..31652002-chr20:31652342..31655282,4	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11696307	0.81[CHB][hapmap]
rs11696310	0.81[CHB][hapmap]
rs11699009	0.81[CHB][hapmap]
rs11700200	0.80[MEX][hapmap]
rs13044428	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs1972199	0.83[ASN][1000 genomes]
rs2024934	0.80[MEX][hapmap]
rs2057261	0.81[CHB][hapmap]
rs2057262	0.81[CHB][hapmap]
rs2070325	0.81[CHB][hapmap]
rs2073325	1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2093067	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221982	0.93[JPT][hapmap]
rs2424936	0.93[JPT][hapmap]
rs2424942	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2424945	1.00[CHB][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs2424946	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2424947	1.00[CHB][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs2424953	0.81[CHB][hapmap]
rs2889732	0.81[CHB][hapmap]
rs372054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4911290	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs4911291	0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs4911292	0.93[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs4911293	0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4911295	0.87[ASN][1000 genomes]
rs4911296	0.87[ASN][1000 genomes]
rs4911297	0.87[ASN][1000 genomes]
rs6057715	0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6057717	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs6059067	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6059069	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs6059079	0.81[CHB][hapmap]
rs6088084	0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs6088085	0.93[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6088091	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs6141876	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs6141877	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs761935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056411	chr20:31057037-31942835	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2758519	chr20:31495807-31748166	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758792	chr20:31495807-31748166	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv3352	chr20:31609939-31654756	Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv912842	chr20:31619922-31651583	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1062857	chr20:31620361-31654093	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs398444	C20orf152	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:31643800-31657000	Weak transcription	Spleen	Spleen
2	chr20:31645600-31650200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:31648200-31653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:31648800-31650600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr20:31648800-31651800	Enhancers	Fetal Muscle Trunk	muscle
6	chr20:31649000-31650000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:31649000-31651600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:31649600-31651200	Enhancers	Adipose Nuclei	Adipose
9	chr20:31649600-31651400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr20:31649600-31651400	Enhancers	Fetal Muscle Leg	muscle

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