Variant report

Variant	rs12322783
Chromosome Location	chr12:49678529-49678530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49677467..49679581-chr12:49679946..49682245,2	K562	blood:
2	chr12:49677107..49685653-chr12:49686694..49692276,10	MCF-7	breast:
3	chr12:49674974..49678602-chr12:49682204..49684622,3	MCF-7	breast:
4	chr12:49676556..49679894-chr12:49730163..49733307,3	MCF-7	breast:
5	chr12:49665631..49676200-chr12:49678297..49684493,17	K562	blood:

Variant related genes	Relation type
ENSG00000135406	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000186897	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11168967	0.86[MEX][hapmap]
rs11168973	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11503617	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11835037	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs12315095	0.81[EUR][1000 genomes]
rs12315130	0.81[EUR][1000 genomes]
rs12322335	0.93[CEU][hapmap];0.93[MEX][hapmap]
rs12580931	0.89[ASW][hapmap];0.88[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2070760	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2236746	0.93[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs28493849	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28691217	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898502	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4898515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61023481	0.81[EUR][1000 genomes]
rs67236923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67309388	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68030039	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136538	0.81[EUR][1000 genomes]
rs7294873	0.81[EUR][1000 genomes]
rs7295247	0.93[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs73112143	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7342318	0.93[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7342384	0.93[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	esv19135	chr12:49676002-49690399	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12322783	PRPH	cis	cerebellum	SCAN
rs12322783	MCRS1	cis	cerebellum	SCAN
rs12322783	TMEM117	cis	cerebellum	SCAN
rs12322783	CXorf26	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49668600-49682400	Weak transcription	HMEC	breast
2	chr12:49677600-49678800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr12:49678000-49678600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:49678000-49678800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:49678000-49678800	Enhancers	HSMMtube	muscle
6	chr12:49678200-49686800	Weak transcription	HSMM	muscle
7	chr12:49678400-49678800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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