Variant report

Variant	rs2054902
Chromosome Location	chr12:48724778-48724779
allele	A/C
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
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1074174	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783231	0.81[JPT][hapmap]
rs10783232	0.81[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs10783239	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168451	0.81[JPT][hapmap]
rs11168455	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs12822085	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs1387256	0.84[EUR][1000 genomes]
rs1489111	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1552551	0.87[EUR][1000 genomes]
rs1906717	0.88[CEU][hapmap]
rs1906718	0.88[ASN][1000 genomes]
rs2130095	0.80[ASN][1000 genomes]
rs2130096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2258342	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2468947	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468948	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2468950	0.93[EUR][1000 genomes]
rs2634669	0.95[EUR][1000 genomes]
rs2634674	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2634679	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2634699	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2634701	0.87[ASN][1000 genomes]
rs2732440	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2732443	0.87[ASN][1000 genomes]
rs2732446	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2732451	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2732455	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2732458	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs2732460	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2732464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2732474	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732475	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732476	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2732477	0.92[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732478	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2732487	0.84[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932090	0.95[EUR][1000 genomes]
rs2932106	0.82[ASN][1000 genomes]
rs2932107	0.87[ASN][1000 genomes]
rs2956704	0.88[ASN][1000 genomes]
rs3989427	0.85[ASN][1000 genomes]
rs4075913	0.81[JPT][hapmap]
rs4760620	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs4760623	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760692	0.85[JPT][hapmap]
rs4760698	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs60908321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580660	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7134201	0.88[ASN][1000 genomes]
rs7134565	0.80[ASN][1000 genomes]
rs7304709	0.86[ASN][1000 genomes]
rs7315258	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs7485057	0.81[JPT][hapmap]
rs7953726	0.84[EUR][1000 genomes]
rs7969749	0.81[JPT][hapmap]
rs901962	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs901963	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs901964	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9645811	0.86[ASN][1000 genomes]
rs987986	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	esv3501066	chr12:48724605-48729122	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
11	nsv438208	chr12:48724778-48734609	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2054902	ASB8	cis	parietal	SCAN
rs2054902	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:4 , 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
4	chr12:48724600-48725200	Enhancers	Hela-S3	cervix

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