Variant report

Variant	rs12322506
Chromosome Location	chr12:49678271-49678272
allele	A/C
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:

Variant related genes	Relation type
ENSG00000135406	Chromatin interaction
ENSG00000186897	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10875946	0.84[AMR][1000 genomes]
rs10875948	0.84[AMR][1000 genomes]
rs11168972	0.84[AMR][1000 genomes]
rs12299403	0.82[EUR][1000 genomes]
rs12299406	0.82[EUR][1000 genomes]
rs12306969	0.98[ASN][1000 genomes]
rs12310595	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318618	0.84[AMR][1000 genomes]
rs12322497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322501	1.00[ASN][1000 genomes]
rs12580095	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582651	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582657	1.00[ASN][1000 genomes]
rs12582901	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382953	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898502	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57755392	0.84[AMR][1000 genomes]
rs58456199	0.85[ASN][1000 genomes]
rs60174686	0.82[AMR][1000 genomes]
rs73307948	0.82[EUR][1000 genomes]
rs7398252	0.82[AMR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12322506	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49668600-49682400	Weak transcription	HMEC	breast
2	chr12:49677400-49678400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:49677600-49678800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:49677800-49678400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49677800-49678400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:49678000-49678400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:49678000-49678600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:49678000-49678800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:49678000-49678800	Enhancers	HSMMtube	muscle
10	chr12:49678200-49686800	Weak transcription	HSMM	muscle

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