Variant report

Variant	rs7972979
Chromosome Location	chr12:122662856-122662857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122662769-122662914	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122661637..122664175-chr12:122674648..122677417,2	K562	blood:
2	chr12:122661637..122663499-chr12:122674584..122677417,2	K562	blood:

Variant related genes	Relation type
LRRC43	TF binding region
IL31	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1047796	0.87[MEX][hapmap]
rs1047813	0.87[MEX][hapmap]
rs10744335	0.91[MEX][hapmap]
rs10847516	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11058789	0.88[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11059094	0.91[MEX][hapmap]
rs11059472	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11059505	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059675	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11608363	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12816786	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461580	0.91[MEX][hapmap]
rs28605425	0.91[MEX][hapmap]
rs28652632	0.91[MEX][hapmap]
rs4040811	0.84[ASN][1000 genomes]
rs4372487	0.88[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4758685	0.87[MEX][hapmap]
rs4758690	0.91[MEX][hapmap]
rs6489217	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489244	0.87[MEX][hapmap]
rs7305669	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485447	0.91[MEX][hapmap]
rs7487608	0.91[MEX][hapmap]
rs7953139	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7955910	0.82[ASN][1000 genomes]
rs7968808	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972875	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7972979	PSMD9	cis	cerebellum	SCAN
rs7972979	P2RX4	cis	parietal	SCAN
rs7972979	GPR81	cis	cerebellum	SCAN
rs7972979	MLXIP	Cis_1M	lymphoblastoid	RTeQTL
rs7972979	ACER3	trans	brain	seeQTL
rs7972979	FAM101A	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122658600-122667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122658800-122667400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:122661200-122665000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:122661400-122665000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:122661600-122664600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:122661600-122665000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:122662200-122667200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:122662400-122667200	Weak transcription	Liver	Liver
9	chr12:122662400-122667200	Weak transcription	Fetal Intestine Large	intestine
10	chr12:122662400-122667200	Weak transcription	Fetal Intestine Small	intestine
11	chr12:122662800-122663000	Enhancers	HepG2	liver

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