Variant report

Variant	rs60255931
Chromosome Location	chr3:20034462-20034463
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:20024849-20034675	K562	blood:	n/a	n/a
2	POLR2A	chr3:20034388-20034497	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20027470..20029591-chr3:20033923..20036338,3	K562	blood:
2	chr3:19987801..19990677-chr3:20032427..20034907,3	MCF-7	breast:

Variant related genes	Relation type
RNU4-85P	TF binding region
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11128927	0.87[ASN][1000 genomes]
rs11128928	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11128929	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11128930	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11128931	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1143451	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629485	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631435	0.91[EUR][1000 genomes]
rs13065319	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068289	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13072891	0.88[ASN][1000 genomes]
rs13076973	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077307	0.81[ASN][1000 genomes]
rs13078505	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082980	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086159	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13089853	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13093485	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13097697	0.88[EUR][1000 genomes]
rs13098388	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17181400	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17181862	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17796115	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34305656	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34343204	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34417128	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34705953	0.84[ASN][1000 genomes]
rs34872212	0.90[EUR][1000 genomes]
rs35175665	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35482904	0.91[ASN][1000 genomes]
rs35684714	0.90[EUR][1000 genomes]
rs35713165	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4610240	0.87[EUR][1000 genomes]
rs59086970	0.83[ASN][1000 genomes]
rs59608170	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775254	0.83[EUR][1000 genomes]
rs6796425	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71316239	0.88[EUR][1000 genomes]
rs7434271	0.88[EUR][1000 genomes]
rs7614695	0.88[ASN][1000 genomes]
rs7615145	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7618928	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633940	0.88[ASN][1000 genomes]
rs7634934	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643167	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7646128	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9877801	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878879	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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
10	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60255931	EFHB	cis	Artery Tibial	GTEx
rs60255931	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs60255931	EFHB	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
2	chr3:20023000-20045800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:20024000-20041400	Weak transcription	Ovary	ovary
4	chr3:20024200-20036800	Weak transcription	Aorta	Aorta
5	chr3:20024200-20051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:20026400-20040800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:20027400-20036200	Weak transcription	NH-A	brain
8	chr3:20027600-20036000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:20030000-20035000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:20030000-20038600	Weak transcription	Fetal Thymus	thymus

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