Variant report

Variant	rs2385142
Chromosome Location	chr7:103869191-103869192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103858966..103860906-chr7:103867973..103872038,3	K562	blood:
2	chr7:103858966..103863231-chr7:103865702..103869473,3	K562	blood:
3	chr7:103848155..103849804-chr7:103868628..103871068,2	MCF-7	breast:
4	chr7:103846534..103850528-chr7:103863639..103871951,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164815	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10238218	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10275259	0.89[ASN][1000 genomes]
rs10487190	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10487191	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11764162	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11767680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11771050	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11771108	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11771398	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773044	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11773664	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17159937	0.87[YRI][hapmap]
rs17324174	0.80[AMR][1000 genomes]
rs17326187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17327021	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17327119	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17377164	0.94[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17377990	0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs2014811	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058722	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299405	0.80[AMR][1000 genomes]
rs2299406	0.94[GIH][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2299410	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2299412	0.91[ASN][1000 genomes]
rs2299413	0.91[ASN][1000 genomes]
rs2299414	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2299415	0.91[ASN][1000 genomes]
rs3779515	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs3779516	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3779517	0.96[EUR][1000 genomes]
rs3808003	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs3808004	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4141408	0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs56950973	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6950715	0.82[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6961789	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6964461	0.80[AMR][1000 genomes]
rs6977598	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73189317	0.80[AMR][1000 genomes]
rs73191412	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73191421	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7784705	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7804341	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7807600	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9656091	0.91[ASN][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	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	nsv1029571	chr7:103855890-103909757	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv608066	chr7:103861035-103916484	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv429789	chr7:103862259-103909757	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2385142	AP4M1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103865000-103870200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:103865200-103869600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:103865200-103871000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:103865200-103871800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:103869000-103870000	Enhancers	Stomach Mucosa	stomach

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