Variant report

Variant	rs12213869
Chromosome Location	chr6:33568687-33568688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33567572..33569907-chr6:33573549..33575919,2	MCF-7	breast:
2	chr6:33566688..33568911-chr6:33636835..33638571,2	K562	blood:
3	chr6:33567428..33569467-chr6:33588119..33589840,2	MCF-7	breast:
4	chr6:33567331..33570244-chr6:33587818..33589464,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10947411	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12202102	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12204232	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206050	0.87[GIH][hapmap];0.86[EUR][1000 genomes]
rs12209172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210212	0.83[ASN][1000 genomes]
rs3846855	0.83[EUR][1000 genomes]
rs4713636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713637	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs471461	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493063	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501084	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502235	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs508298	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs510153	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511007	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs523852	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs523892	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs525819	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550127	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562027	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574186	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5745568	0.87[GIH][hapmap]
rs5745582	0.87[GIH][hapmap]
rs9296095	0.87[GIH][hapmap]

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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
5	esv992246	chr6:33561708-33570974	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv5250	chr6:33565017-33598370	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12213869	CDKN1A	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33559600-33569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:33561600-33570400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:33566000-33571000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:33567600-33569800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:33567600-33571400	Weak transcription	Psoas Muscle	Psoas
6	chr6:33567600-33571600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:33567600-33572800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:33567600-33572800	Weak transcription	A549	lung
9	chr6:33567600-33572800	Weak transcription	HSMMtube	muscle
10	chr6:33567600-33574200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:33567600-33575800	Weak transcription	Right Atrium	heart
12	chr6:33567600-33575800	Weak transcription	Right Ventricle	heart
13	chr6:33567800-33568800	Enhancers	Hela-S3	cervix
14	chr6:33567800-33569800	Weak transcription	Left Ventricle	heart
15	chr6:33567800-33570800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:33567800-33571800	Weak transcription	Lung	lung
17	chr6:33567800-33572800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:33567800-33574400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:33567800-33575000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:33567800-33575400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:33568200-33568800	Enhancers	Placenta	Placenta
22	chr6:33568600-33568800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:33568600-33571600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:33568600-33574400	Weak transcription	HMEC	breast

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