Variant report

Variant	rs12202785
Chromosome Location	chr6:167057463-167057464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167040717..167042560-chr6:167055383..167058084,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071242	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10946178	0.81[TSI][hapmap]
rs12199983	0.80[EUR][1000 genomes]
rs12203904	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12215660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2223405	0.87[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2223406	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs3778367	0.91[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3778369	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs3778370	0.83[JPT][hapmap]
rs3778373	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs3778375	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs3799570	0.83[JPT][hapmap]
rs6909011	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6911301	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6919949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752989	0.82[CHD][hapmap]
rs874153	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9348158	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9348166	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9348167	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9356498	0.85[EUR][1000 genomes]
rs9364864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366034	0.85[EUR][1000 genomes]
rs9366035	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9459709	0.87[CEU][hapmap];0.90[EUR][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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023649	chr6:167026469-167060732	Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12202785	RNASET2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167043400-167058200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:167045000-167061200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:167047600-167061200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:167054400-167059400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:167054400-167061400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:167054600-167061400	Weak transcription	Fetal Heart	heart
7	chr6:167054600-167061400	Weak transcription	Gastric	stomach
8	chr6:167054600-167062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:167054600-167063000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:167054600-167063000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:167054800-167061200	Weak transcription	Fetal Kidney	kidney
12	chr6:167054800-167062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:167056600-167062800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:167057400-167057600	Enhancers	Left Ventricle	heart
15	chr6:167057400-167057800	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr6:167057400-167058400	Enhancers	HUVEC	blood vessel

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