Variant report

Variant	rs10056561
Chromosome Location	chr5:111542683-111542684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10043186	0.86[EUR][1000 genomes]
rs10054560	0.82[EUR][1000 genomes]
rs10069011	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1078128	0.89[EUR][1000 genomes]
rs1078129	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11241153	0.91[EUR][1000 genomes]
rs13165611	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560053	0.82[EUR][1000 genomes]
rs1560054	0.82[EUR][1000 genomes]
rs1560055	0.82[EUR][1000 genomes]
rs1560057	0.81[EUR][1000 genomes]
rs1560058	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17134228	0.97[ASN][1000 genomes]
rs17134250	0.99[ASN][1000 genomes]
rs1863960	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981954	0.82[EUR][1000 genomes]
rs2114988	0.82[ASN][1000 genomes]
rs2114989	0.81[ASN][1000 genomes]
rs2162733	0.99[ASN][1000 genomes]
rs2303657	0.99[ASN][1000 genomes]
rs2416277	0.89[EUR][1000 genomes]
rs3797320	0.94[ASN][1000 genomes]
rs3815896	0.92[ASN][1000 genomes]
rs4957632	0.81[EUR][1000 genomes]
rs4957634	0.88[EUR][1000 genomes]
rs4957636	0.86[EUR][1000 genomes]
rs4958002	0.81[EUR][1000 genomes]
rs4958003	0.81[EUR][1000 genomes]
rs4958004	0.81[EUR][1000 genomes]
rs4958007	0.83[EUR][1000 genomes]
rs4958008	0.82[EUR][1000 genomes]
rs4958009	0.84[EUR][1000 genomes]
rs4958010	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4958012	0.88[EUR][1000 genomes]
rs4958013	0.89[EUR][1000 genomes]
rs4958014	0.89[EUR][1000 genomes]
rs4958015	0.93[EUR][1000 genomes]
rs59537089	0.90[EUR][1000 genomes]
rs6594569	0.80[AMR][1000 genomes]
rs6594574	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6863063	0.82[EUR][1000 genomes]
rs6873159	0.99[ASN][1000 genomes]
rs6876893	0.91[EUR][1000 genomes]
rs6884589	0.88[EUR][1000 genomes]
rs7704087	0.88[EUR][1000 genomes]
rs7706160	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7709484	0.92[EUR][1000 genomes]
rs7710973	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7711158	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7716309	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7717363	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7719346	0.90[EUR][1000 genomes]
rs890757	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs890758	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10056561	EPB41L4A	cis	Nerve Tibial	GTEx
rs10056561	EPB41L4A	cis	brain	BrainEAC

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
2	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
3	chr5:111502800-111546000	Weak transcription	Ovary	ovary
4	chr5:111504800-111557800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:111504800-111586400	Weak transcription	Gastric	stomach
6	chr5:111510800-111547400	Weak transcription	HUVEC	blood vessel
7	chr5:111519000-111546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:111519200-111553800	Weak transcription	Pancreas	Pancrea
9	chr5:111519800-111553600	Weak transcription	Esophagus	oesophagus
10	chr5:111529800-111553600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:111538000-111553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:111538200-111543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:111538200-111546400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:111538600-111544800	Weak transcription	Fetal Kidney	kidney
15	chr5:111538600-111563600	Weak transcription	Lung	lung
16	chr5:111539000-111553600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:111539400-111553200	Weak transcription	NHEK	skin
18	chr5:111540400-111544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:111540400-111553600	Weak transcription	Fetal Heart	heart
20	chr5:111541800-111542800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:111541800-111542800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:111541800-111543000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:111541800-111553800	Weak transcription	Right Ventricle	heart
24	chr5:111542000-111544200	Weak transcription	Left Ventricle	heart
25	chr5:111542200-111542800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:111542200-111544400	Weak transcription	K562	blood
27	chr5:111542400-111546200	Weak transcription	Hela-S3	cervix
28	chr5:111542400-111546400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:111542400-111546400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr5:111542600-111543000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:111542600-111545000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:111542600-111546400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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