Variant report

Variant	rs2548417
Chromosome Location	chr5:96534619-96534620
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96533022..96535910-chr5:96537589..96540065,2	K562	blood:
2	chr5:96534501..96536985-chr5:96538534..96540888,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10040634	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10045981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10054131	0.90[ASN][1000 genomes]
rs10055532	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10057166	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10069145	0.91[ASN][1000 genomes]
rs10075312	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10476700	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11135494	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11135495	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11135496	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12055294	0.91[ASN][1000 genomes]
rs12516613	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12519482	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653352	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12657849	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs167590	0.85[ASN][1000 genomes]
rs172741	0.85[ASN][1000 genomes]
rs2081141	0.91[ASN][1000 genomes]
rs2544777	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548413	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2548418	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs317111	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs61264046	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61342674	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62377144	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7705103	0.90[ASN][1000 genomes]
rs7709067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7730273	0.90[ASN][1000 genomes]
rs9314191	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9314196	0.90[ASN][1000 genomes]
rs9918187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[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	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2548417	FAM172A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96520000-96534800	Weak transcription	Left Ventricle	heart
2	chr5:96530400-96537000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:96530400-96537400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:96530600-96535200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:96530600-96536600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr5:96533000-96534800	Strong transcription	Primary B cells from cord blood	blood
7	chr5:96533600-96534800	Genic enhancers	Dnd41	blood

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