Variant report

Variant	rs548349
Chromosome Location	chr12:123224909-123224910
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	chr12:123174042..123175689-chr12:123223444..123225205,2	MCF-7	breast:
2	chr12:123223583..123226017-chr12:123227504..123229824,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs11059729	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1260121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[TSI][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6489241	1.00[CEU][hapmap]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs839352	0.83[AMR][1000 genomes]
rs839354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs839362	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs548349	TMEM120B	cis	parietal	SCAN
rs548349	KDM2B	cis	cerebellum	SCAN
rs548349	RAB35	cis	parietal	SCAN
rs548349	EIF2B1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123222200-123225400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:123223200-123227200	Weak transcription	HepG2	liver
3	chr12:123223400-123226800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:123223400-123227400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:123224000-123226800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:123224600-123225400	Enhancers	K562	blood
7	chr12:123224800-123225200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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