Variant report

Variant	rs10872562
Chromosome Location	chr6:143974930-143974931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143966000..143968139-chr6:143973368..143975325,2	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]
rs1108314	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs11155315	0.86[CHB][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11155317	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198291	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206069	0.87[ASN][1000 genomes]
rs12207002	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208927	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12528456	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3924969	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934959	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6901659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907410	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6913134	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6915784	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931801	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs7740709	0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs7741424	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748882	0.86[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7766510	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7769294	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7772565	0.86[CHB][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7776119	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8180640	0.89[ASN][1000 genomes]
rs9373396	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373397	0.94[JPT][hapmap]
rs9376776	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376779	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9386042	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs9386043	0.94[JPT][hapmap]
rs9390126	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399458	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403521	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403523	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496739	0.85[CHD][hapmap]

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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517253	chr6:143953672-143975157	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10872562	PTPRN2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143959000-143978400	Weak transcription	Left Ventricle	heart
2	chr6:143973000-143980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:143973600-143975000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:143973600-143975000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr6:143974200-143976200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:143974200-143981600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:143974400-143975800	Weak transcription	Aorta	Aorta
8	chr6:143974400-143978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:143974400-143978800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:143974400-143980600	Weak transcription	Gastric	stomach
11	chr6:143974400-143980600	Weak transcription	Psoas Muscle	Psoas
12	chr6:143974600-143975400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:143974600-143976400	Weak transcription	HepG2	liver
14	chr6:143974600-143976800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:143974600-143984400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:143974800-143978600	Weak transcription	Fetal Intestine Small	intestine

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