Variant report

Variant	rs2460050
Chromosome Location	chr11:93754227-93754228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr11:93754178-93754570	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:93754053-93754495	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr11:93754169-93754442	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr11:93754057-93754526	MCF10A-Er-Src	breast:	n/a	n/a
5	SETDB1	chr11:93753956-93754348	U2OS	brain:	n/a	n/a
6	FOS	chr11:93753967-93754496	MCF10A-Er-Src	breast:	n/a	n/a
7	KAP1	chr11:93754006-93754272	U2OS	brain:	n/a	n/a
8	MYC	chr11:93754199-93754466	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr11:93754053-93754526	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:93754223-93754273	Caco-2	colon:	n/a
2	chr11:93754223-93754273	MCF-7	breast:	n/a
3	chr11:93754223-93754273	HRE	kidney:	n/a
4	chr11:93754223-93754273	AG09309	skin:	n/a
5	chr11:93754223-93754273	NHBE	bronchial:	n/a
6	chr11:93754223-93754273	Hepatocyte	liver:	n/a
7	chr11:93754223-93754273	H1-hESC	embryonic stem cell:	embryo
8	chr11:93754223-93754273	SKMC	muscle:	n/a
9	chr11:93754223-93754273	HNPCEpiC	eye:	n/a
10	chr11:93754223-93754273	ovcar-3	ovarian:	n/a
11	chr11:93754223-93754273	AG09319	gingival:	n/a
12	chr11:93754223-93754273	HCPEpiC	choroid plexus:	n/a
13	chr11:93754223-93754273	GM12878	blood:	n/a
14	chr11:93754223-93754273	AG04449	skin:	fetal
15	chr11:93754223-93754273	HCT-116	colon:	n/a
16	chr11:93754223-93754273	GM12891	blood:	n/a
17	chr11:93754223-93754273	PANC-1	pancreas:	n/a
18	chr11:93754223-93754273	PFSK-1	brain:	n/a
19	chr11:93754223-93754273	SK-N-SH	brain:	n/a
20	chr11:93754223-93754273	U87	brain:	n/a
21	chr11:93754223-93754273	HCF	heart:	n/a
22	chr11:93754223-93754273	HIPEpiC	eye:	n/a
23	chr11:93754223-93754273	HEK293	kidney:	embryo
24	chr11:93754223-93754273	NT2-D1	testis:	n/a
25	chr11:93754223-93754273	PrEC	prostate:	n/a
26	chr11:93754223-93754273	HCM	heart:	n/a
27	chr11:93754223-93754273	K562	blood:	n/a
28	chr11:93754223-93754273	HUVEC	blood vessel:	n/a
29	chr11:93754223-93754273	NB4	blood:	n/a
30	chr11:93754223-93754273	BJ	skin:	n/a
31	chr11:93754223-93754273	GM19239	blood:	n/a
32	chr11:93754223-93754273	ProgFib	skin:	n/a
33	chr11:93754223-93754273	GM06990	blood:	n/a
34	chr11:93754223-93754273	AoSMC	blood vessel:	n/a
35	chr11:93754223-93754273	MCF10A-Er-Src	breast:	n/a
36	chr11:93754223-93754273	SAEC	small airway:	n/a
37	chr11:93754223-93754273	HRPEpiC	eye:	n/a
38	chr11:93754223-93754273	Jurkat	blood:	n/a
39	chr11:93754223-93754273	IMR90	lung:	fetal
40	chr11:93754223-93754273	AG10803	skin:	n/a
41	chr11:93754223-93754273	GM12892	blood:	n/a
42	chr11:93754223-93754273	SK-N-SH_RA	brain:	n/a
43	chr11:93754223-93754273	HAEpiC	amniotic membrane:	n/a
44	chr11:93754223-93754273	HEEpiC	esophagus:	n/a
45	chr11:93754223-93754273	NH-A	brain:	n/a
46	chr11:93754223-93754273	A549	lung:	n/a
47	chr11:93754223-93754273	BE2_C	brain:	n/a
48	chr11:93754223-93754273	CMK	blood:	n/a
49	chr11:93754223-93754273	LNCaP	prostate:	n/a
50	chr11:93754223-93754273	AG04450	lung:	fetal

No data

Variant related genes	Relation type
HEPHL1	TF binding region
HEPHL1	CpG island

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10501813	0.95[ASN][1000 genomes]
rs11820915	0.83[EUR][1000 genomes]
rs11823303	0.85[EUR][1000 genomes]
rs11825709	0.90[ASN][1000 genomes]
rs11828737	0.83[EUR][1000 genomes]
rs1401184	0.95[ASN][1000 genomes]
rs1518560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518565	0.82[EUR][1000 genomes]
rs1518566	0.82[EUR][1000 genomes]
rs1568259	0.83[EUR][1000 genomes]
rs1589166	0.95[ASN][1000 genomes]
rs1607401	0.95[ASN][1000 genomes]
rs16919810	0.85[EUR][1000 genomes]
rs16919815	0.85[EUR][1000 genomes]
rs16919858	0.81[EUR][1000 genomes]
rs1850656	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894165	0.95[ASN][1000 genomes]
rs1894166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1914723	0.83[EUR][1000 genomes]
rs1945786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1945787	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2020351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102857	0.95[ASN][1000 genomes]
rs2139089	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176563	0.95[ASN][1000 genomes]
rs2203793	0.95[ASN][1000 genomes]
rs2213108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213110	0.93[ASN][1000 genomes]
rs2399749	0.83[EUR][1000 genomes]
rs2399750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2456556	0.89[EUR][1000 genomes]
rs2460049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460053	0.95[ASN][1000 genomes]
rs2460064	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460065	0.95[ASN][1000 genomes]
rs2460069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460070	0.95[ASN][1000 genomes]
rs2462733	0.95[ASN][1000 genomes]
rs2462735	0.95[ASN][1000 genomes]
rs2462756	0.94[ASN][1000 genomes]
rs2462757	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462758	0.95[ASN][1000 genomes]
rs2462759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2462760	0.94[ASN][1000 genomes]
rs2462763	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511380	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511381	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2511403	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511411	0.95[ASN][1000 genomes]
rs4415716	0.83[EUR][1000 genomes]
rs56355412	0.83[EUR][1000 genomes]
rs56938392	0.94[ASN][1000 genomes]
rs57106172	0.90[ASN][1000 genomes]
rs57586533	0.90[ASN][1000 genomes]
rs57953549	0.84[ASN][1000 genomes]
rs59689949	0.90[ASN][1000 genomes]
rs59793398	0.94[ASN][1000 genomes]
rs66514329	0.95[ASN][1000 genomes]
rs66523751	0.82[ASN][1000 genomes]
rs66538341	0.90[ASN][1000 genomes]
rs66977226	0.90[ASN][1000 genomes]
rs67001808	0.94[ASN][1000 genomes]
rs67243356	0.90[ASN][1000 genomes]
rs67412659	0.94[ASN][1000 genomes]
rs67988338	0.90[ASN][1000 genomes]
rs7107851	0.85[EUR][1000 genomes]
rs72964631	0.94[ASN][1000 genomes]
rs72964645	0.94[ASN][1000 genomes]
rs72964666	0.95[ASN][1000 genomes]
rs72964672	0.81[EUR][1000 genomes]
rs72964674	0.83[EUR][1000 genomes]
rs72964683	0.83[EUR][1000 genomes]
rs72964690	0.83[EUR][1000 genomes]
rs72964693	0.83[EUR][1000 genomes]
rs72966608	0.85[EUR][1000 genomes]
rs72966612	0.83[EUR][1000 genomes]
rs72966637	0.85[EUR][1000 genomes]
rs73551180	0.82[ASN][1000 genomes]
rs73564796	0.94[ASN][1000 genomes]
rs73564799	0.94[ASN][1000 genomes]
rs959342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959343	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978777	0.94[ASN][1000 genomes]
rs989088	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049467	chr11:93651025-93778717	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv898183	chr11:93725384-93906735	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2460050	HEPHL1	cis	Artery Aorta	GTEx
rs2460050	HEPHL1	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93749600-93754400	Enhancers	HMEC	breast
2	chr11:93750400-93754800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:93752200-93758000	Weak transcription	NH-A	brain
4	chr11:93753800-93755800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:93753800-93756200	Flanking Active TSS	NHEK	skin
6	chr11:93754000-93756200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:93754200-93754800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:93754200-93754800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:93754200-93754800	Enhancers	Aorta	Aorta

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