Variant report

Variant	rs2054903
Chromosome Location	chr12:48724493-48724494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48595137..48597304-chr12:48723184..48725728,2	K562	blood:
2	chr12:48723401..48726015-chr12:48731031..48733987,2	K562	blood:
3	chr12:48723517..48726373-chr12:48743462..48746154,2	MCF-7	breast:
4	chr12:48724124..48726924-chr12:48729668..48731393,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172640	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1021313	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431526	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10437919	0.82[ASN][1000 genomes]
rs10437920	0.82[ASN][1000 genomes]
rs10467101	0.84[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875767	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10875770	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs10875772	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875777	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875778	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875779	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875792	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875793	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875799	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168459	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs11168487	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168493	0.84[ASN][1000 genomes]
rs11168508	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168510	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168514	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168516	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168520	0.97[ASN][1000 genomes]
rs11168536	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227601	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12313745	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12317751	0.82[ASN][1000 genomes]
rs12322347	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12322348	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1471997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122812	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs2054904	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279464	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2450992	0.91[ASN][1000 genomes]
rs2634675	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2732439	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2732465	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2898065	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3185921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760625	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61941003	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61941006	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580659	0.85[JPT][hapmap]
rs716553	0.82[ASN][1000 genomes]
rs7297298	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7303055	0.82[ASN][1000 genomes]
rs7486008	0.82[ASN][1000 genomes]
rs9634261	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9788082	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2054903	FAM186B	cis	parietal	SCAN
rs2054903	ZNF641	cis	cerebellum	SCAN
rs2054903	ASB8	cis	cerebellum	SCAN
rs2054903	TMEM106C	cis	cerebellum	SCAN
rs2054903	H1FNT	cis	cerebellum	SCAN
rs2054903	RP1-228P16.1	cis	Thyroid	GTEx
rs2054903	RND1	cis	cerebellum	SCAN
rs2054903	ZNF641	cis	Muscle Skeletal	GTEx
rs2054903	PFKM	cis	parietal	SCAN
rs2054903	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs2054903	IRAK4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48723800-48736600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48724200-48734400	Weak transcription	Thymus	Thymus
3	chr12:48724400-48736000	Weak transcription	Fetal Stomach	stomach

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