Variant report

Variant	rs2099446
Chromosome Location	chr7:99471072-99471073
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	chr7:99470145..99472550-chr7:99473069..99474850,2	K562	blood:

Variant related genes	Relation type
ENSG00000244623	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10235630	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1025576	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1121592	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1865472	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2060452	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2082744	0.84[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2082745	0.84[ASN][1000 genomes]
rs2099445	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247762	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2527881	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2527900	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2527902	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2527904	0.86[EUR][1000 genomes]
rs2527908	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2527912	0.89[EUR][1000 genomes]
rs2527914	0.81[JPT][hapmap]
rs2527918	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2527920	0.89[EUR][1000 genomes]
rs2527925	0.84[ASN][1000 genomes]
rs2527927	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2571995	0.86[EUR][1000 genomes]
rs2572000	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2572002	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2572011	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2572015	0.84[ASN][1000 genomes]
rs2572018	0.84[ASN][1000 genomes]
rs2572019	0.84[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2572022	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2572023	0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs2572024	0.84[ASN][1000 genomes]
rs4727439	0.86[EUR][1000 genomes]
rs474229	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs503115	0.96[ASN][1000 genomes]
rs7781442	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	esv1792388	chr7:99468155-99497338	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2099446	PILRB	cis	parietal	SCAN
rs2099446	OR2AE1	cis	cerebellum	SCAN
rs2099446	TRIM4	cis	Artery Tibial	GTEx
rs2099446	ORAI2	cis	parietal	SCAN
rs2099446	TRIM4	cis	multi-tissue	Pritchard
rs2099446	TRIM4	cis	Thyroid	GTEx
rs2099446	OR2AE1	cis	parietal	SCAN
rs2099446	TRIM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99458200-99489600	Weak transcription	Pancreas	Pancrea
2	chr7:99465200-99475400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:99468400-99487200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:99470000-99489600	Weak transcription	Gastric	stomach
5	chr7:99470400-99486800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:99470400-99487000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:99470600-99474000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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