Variant report

Variant	rs883229
Chromosome Location	chr12:66850514-66850515
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	chr12:66840883..66843625-chr12:66848449..66851341,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10219502	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219504	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219746	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748046	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784542	0.83[AMR][1000 genomes]
rs10878426	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878427	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878428	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878429	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878430	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878431	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878432	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11176189	0.87[ASN][1000 genomes]
rs11176194	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176198	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176208	0.92[CEU][hapmap];0.87[AMR][1000 genomes]
rs11176216	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11835627	0.90[ASN][1000 genomes]
rs12322827	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12366637	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12366955	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371843	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809616	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12817312	0.87[AMR][1000 genomes]
rs1826545	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2904515	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3891950	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4128160	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309214	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs866954	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs883230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952562	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952563	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs883229	PPM1H	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66823200-66859000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:66836200-66856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:66836400-66855200	Weak transcription	Placenta	Placenta
4	chr12:66838800-66858400	Weak transcription	Fetal Brain Female	brain
5	chr12:66843800-66857200	Weak transcription	HMEC	breast
6	chr12:66844000-66861600	Weak transcription	Primary T cells from cord blood	blood
7	chr12:66846800-66852000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:66846800-66860200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:66849400-66866400	Weak transcription	Pancreas	Pancrea
10	chr12:66849600-66852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:66849600-66860000	Weak transcription	Esophagus	oesophagus
12	chr12:66850000-66851200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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