Variant report

Variant	rs13222475
Chromosome Location	chr7:12868301-12868302
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	chr7:12867009..12868914-chr7:12869062..12871956,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10950417	0.82[EUR][1000 genomes]
rs10950418	0.82[EUR][1000 genomes]
rs10950419	0.83[EUR][1000 genomes]
rs12155420	0.81[EUR][1000 genomes]
rs12531011	0.80[EUR][1000 genomes]
rs12531228	0.83[EUR][1000 genomes]
rs12531814	0.83[EUR][1000 genomes]
rs12534712	0.83[EUR][1000 genomes]
rs12535869	0.83[EUR][1000 genomes]
rs12538097	0.81[EUR][1000 genomes]
rs12538194	0.81[EUR][1000 genomes]
rs12538763	0.81[EUR][1000 genomes]
rs12538792	0.88[CEU][hapmap]
rs12539313	0.88[CEU][hapmap]
rs12539387	0.83[EUR][1000 genomes]
rs12699417	0.81[EUR][1000 genomes]
rs12699419	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs12699421	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12699422	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12699426	0.88[CEU][hapmap]
rs13222073	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13224587	0.84[EUR][1000 genomes]
rs13225356	0.85[EUR][1000 genomes]
rs13225358	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13228110	0.83[EUR][1000 genomes]
rs13228635	0.83[EUR][1000 genomes]
rs13232299	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs13233019	0.82[EUR][1000 genomes]
rs13233170	0.82[EUR][1000 genomes]
rs13233911	0.83[EUR][1000 genomes]
rs13236020	0.83[CEU][hapmap]
rs13238922	0.83[EUR][1000 genomes]
rs13244444	0.83[EUR][1000 genomes]
rs17680996	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs17681117	0.81[ASN][1000 genomes]
rs2215334	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28504348	0.84[EUR][1000 genomes]
rs34107937	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34338066	0.80[EUR][1000 genomes]
rs34591294	0.81[EUR][1000 genomes]
rs34809518	0.81[EUR][1000 genomes]
rs34904008	0.84[EUR][1000 genomes]
rs34971219	0.80[EUR][1000 genomes]
rs35003906	0.80[EUR][1000 genomes]
rs35181098	0.81[EUR][1000 genomes]
rs35193720	0.82[EUR][1000 genomes]
rs35290407	0.84[EUR][1000 genomes]
rs35464195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35867430	0.84[EUR][1000 genomes]
rs35917995	0.80[EUR][1000 genomes]
rs35988890	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36003929	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36091229	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55864529	0.84[EUR][1000 genomes]
rs62445809	0.94[ASN][1000 genomes]
rs62445810	0.94[ASN][1000 genomes]
rs62445811	0.94[ASN][1000 genomes]
rs62445812	0.94[ASN][1000 genomes]
rs62445825	0.97[ASN][1000 genomes]
rs62445826	0.97[ASN][1000 genomes]
rs62445827	0.97[ASN][1000 genomes]
rs62445828	0.97[ASN][1000 genomes]
rs62445829	0.97[ASN][1000 genomes]
rs62445831	0.97[ASN][1000 genomes]
rs62445832	0.97[ASN][1000 genomes]
rs62445833	0.97[ASN][1000 genomes]
rs62445834	0.94[ASN][1000 genomes]
rs62445836	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62445837	0.94[ASN][1000 genomes]
rs62445838	0.94[ASN][1000 genomes]
rs62445851	0.84[ASN][1000 genomes]
rs62445853	0.84[ASN][1000 genomes]
rs62445854	0.84[ASN][1000 genomes]
rs62445855	0.84[ASN][1000 genomes]
rs62445856	0.84[ASN][1000 genomes]
rs62445857	0.84[ASN][1000 genomes]
rs62448165	0.84[ASN][1000 genomes]
rs62448166	0.84[ASN][1000 genomes]
rs62448167	0.84[ASN][1000 genomes]
rs62448168	0.84[ASN][1000 genomes]
rs62448170	0.84[ASN][1000 genomes]
rs6460984	0.83[EUR][1000 genomes]
rs6954306	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6954419	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6956351	0.84[ASN][1000 genomes]
rs6960791	0.97[ASN][1000 genomes]
rs6961220	0.97[ASN][1000 genomes]
rs6966108	0.84[ASN][1000 genomes]
rs6966517	0.84[ASN][1000 genomes]
rs71538805	0.82[EUR][1000 genomes]
rs764903	0.84[ASN][1000 genomes]
rs7780699	0.84[ASN][1000 genomes]
rs7781158	1.00[CHB][hapmap]
rs7793712	0.84[ASN][1000 genomes]
rs7796721	0.94[ASN][1000 genomes]
rs9648162	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027806	chr7:12842708-12875714	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13222475	THSD7A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12861200-12868600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:12861800-12871200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:12867200-12868400	Enhancers	NHEK	skin
4	chr7:12867600-12873400	Weak transcription	Pancreas	Pancrea
5	chr7:12868000-12871400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:12868200-12871200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:12868200-12877200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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