Variant report

Variant	rs1031423
Chromosome Location	chr5:93276883-93276884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10044641	0.86[ASN][1000 genomes]
rs10061069	0.87[ASN][1000 genomes]
rs10476590	0.82[CEU][hapmap]
rs10866760	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11135394	0.89[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[ASN][1000 genomes]
rs11135397	0.81[EUR][1000 genomes]
rs11135401	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11948511	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653528	0.81[EUR][1000 genomes]
rs13165221	0.82[ASN][1000 genomes]
rs13167027	0.87[ASN][1000 genomes]
rs13184801	0.82[ASN][1000 genomes]
rs13186432	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1470150	0.81[CEU][hapmap]
rs17083380	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.94[ASN][1000 genomes]
rs2043979	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2045020	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs35672980	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60375544	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6556833	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6869110	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7708175	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7721668	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7727923	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7728825	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs7732578	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7733142	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7735009	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs890738	0.88[ASN][1000 genomes]
rs896729	0.81[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv882384	chr5:93136661-93380123	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1028893	chr5:93213264-93276883	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1020849	chr5:93228065-93279216	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1030870	chr5:93242611-93282996	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1031423	FAM172A	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93194200-93307600	Weak transcription	Left Ventricle	heart
2	chr5:93252200-93284400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr5:93257200-93287400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:93263200-93289200	Weak transcription	Ovary	ovary
5	chr5:93263200-93326400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:93263400-93303800	Weak transcription	HSMMtube	muscle
7	chr5:93268800-93289800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:93270600-93289000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:93270600-93289800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:93272400-93289400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:93274600-93277000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:93276800-93277000	Enhancers	Aorta	Aorta

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