Variant report

Variant	rs890758
Chromosome Location	chr5:111545957-111545958
allele	A/T
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	GATA3	chr5:111545916-111546673	A549	lung:	n/a	chr5:111546407-111546415
2	CTCF	chr5:111545846-111546603	HCT-116	colon:	n/a	chr5:111546295-111546308 chr5:111546292-111546310 chr5:111546294-111546315
3	CTCF	chr5:111545532-111546633	SK-N-SH	brain:	n/a	chr5:111546295-111546308 chr5:111546292-111546310 chr5:111546294-111546315

No.	Distal block	Cell Line	Cell type
1	chr5:111545812..111546719-chr5:111755708..111756545,3	MCF-7	breast:
2	chr5:111545913..111546803-chr5:111702693..111703411,4	MCF-7	breast:
3	chr5:111545766..111546849-chr5:111755716..111756742,6	MCF-7	breast:
4	chr5:111545569..111546326-chr5:111575265..111575942,2	MCF-7	breast:
5	chr5:111545807..111546357-chr5:111755716..111756657,2	K562	blood:
6	chr5:111545649..111546314-chr5:111563458..111564367,2	MCF-7	breast:

Variant related genes	Relation type
EPB41L4A	TF binding region
ENSG00000251076	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10037824	1.00[ASN][1000 genomes]
rs10040749	1.00[ASN][1000 genomes]
rs10043186	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10054560	0.86[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054610	0.87[CEU][hapmap]
rs10056561	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10065740	1.00[ASN][1000 genomes]
rs10068493	1.00[ASN][1000 genomes]
rs10069011	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070995	1.00[ASN][1000 genomes]
rs1020951	1.00[ASN][1000 genomes]
rs10463433	1.00[ASN][1000 genomes]
rs10477478	1.00[ASN][1000 genomes]
rs10478073	1.00[ASN][1000 genomes]
rs1054724	1.00[ASN][1000 genomes]
rs1078128	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241153	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241160	1.00[ASN][1000 genomes]
rs12186685	1.00[ASN][1000 genomes]
rs12187589	1.00[ASN][1000 genomes]
rs12187787	1.00[ASN][1000 genomes]
rs12188700	1.00[ASN][1000 genomes]
rs12189034	1.00[ASN][1000 genomes]
rs13153601	1.00[ASN][1000 genomes]
rs13165611	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1366144	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1427978	1.00[ASN][1000 genomes]
rs1560052	1.00[ASN][1000 genomes]
rs1560053	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560054	0.87[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560055	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560057	0.87[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560058	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560061	1.00[ASN][1000 genomes]
rs17134319	1.00[ASN][1000 genomes]
rs17134348	1.00[ASN][1000 genomes]
rs17271934	1.00[ASN][1000 genomes]
rs17343994	1.00[ASN][1000 genomes]
rs17345175	1.00[ASN][1000 genomes]
rs1863960	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1896620	1.00[ASN][1000 genomes]
rs1896621	1.00[ASN][1000 genomes]
rs1975015	1.00[ASN][1000 genomes]
rs1981954	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2114991	1.00[ASN][1000 genomes]
rs2416277	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27413	1.00[ASN][1000 genomes]
rs386446	1.00[ASN][1000 genomes]
rs4602685	1.00[ASN][1000 genomes]
rs4957632	0.87[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957634	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957636	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958002	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958003	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958004	0.87[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958007	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4958008	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4958009	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958010	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958012	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958013	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958014	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958015	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958020	1.00[ASN][1000 genomes]
rs4958025	1.00[ASN][1000 genomes]
rs55639430	1.00[ASN][1000 genomes]
rs55796748	1.00[ASN][1000 genomes]
rs55829200	1.00[ASN][1000 genomes]
rs55845736	1.00[ASN][1000 genomes]
rs55913426	1.00[ASN][1000 genomes]
rs56108405	1.00[ASN][1000 genomes]
rs56288086	1.00[ASN][1000 genomes]
rs56293447	1.00[ASN][1000 genomes]
rs56307310	1.00[ASN][1000 genomes]
rs56881711	1.00[ASN][1000 genomes]
rs57428532	1.00[ASN][1000 genomes]
rs59537089	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60636568	1.00[ASN][1000 genomes]
rs61061658	1.00[ASN][1000 genomes]
rs62365251	1.00[ASN][1000 genomes]
rs62367266	1.00[ASN][1000 genomes]
rs62372421	1.00[ASN][1000 genomes]
rs6594566	1.00[ASN][1000 genomes]
rs6594567	1.00[ASN][1000 genomes]
rs6594569	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6594571	1.00[ASN][1000 genomes]
rs6594574	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594577	1.00[ASN][1000 genomes]
rs6594588	1.00[ASN][1000 genomes]
rs66521031	1.00[ASN][1000 genomes]
rs66550707	1.00[ASN][1000 genomes]
rs66892745	1.00[ASN][1000 genomes]
rs67033649	1.00[ASN][1000 genomes]
rs67586008	1.00[ASN][1000 genomes]
rs67631852	1.00[ASN][1000 genomes]
rs6863063	0.87[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872947	1.00[ASN][1000 genomes]
rs6876893	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878117	1.00[ASN][1000 genomes]
rs6878423	1.00[ASN][1000 genomes]
rs6884589	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893877	1.00[ASN][1000 genomes]
rs6894036	1.00[ASN][1000 genomes]
rs72781655	1.00[ASN][1000 genomes]
rs72781664	1.00[ASN][1000 genomes]
rs72781668	1.00[ASN][1000 genomes]
rs72781677	1.00[ASN][1000 genomes]
rs72781678	1.00[ASN][1000 genomes]
rs7703522	1.00[ASN][1000 genomes]
rs7704087	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706160	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709484	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710973	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711158	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716309	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717160	1.00[ASN][1000 genomes]
rs7717363	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719346	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722291	1.00[ASN][1000 genomes]
rs821736	1.00[ASN][1000 genomes]
rs821749	1.00[ASN][1000 genomes]
rs890757	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs890758	EPB41L4A	cis	Nerve Tibial	GTEx

Chromatin state (count:29 , 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	chr5:111538200-111546400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:111538600-111563600	Weak transcription	Lung	lung
14	chr5:111539000-111553600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:111539400-111553200	Weak transcription	NHEK	skin
16	chr5:111540400-111553600	Weak transcription	Fetal Heart	heart
17	chr5:111541800-111553800	Weak transcription	Right Ventricle	heart
18	chr5:111542400-111546200	Weak transcription	Hela-S3	cervix
19	chr5:111542400-111546400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:111542400-111546400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:111542600-111546400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:111542800-111546200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:111542800-111553200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:111544600-111553600	Weak transcription	Left Ventricle	heart
25	chr5:111545200-111546400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:111545200-111546400	Weak transcription	K562	blood
27	chr5:111545400-111556800	Weak transcription	Fetal Kidney	kidney
28	chr5:111545600-111546000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:111545600-111556400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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