Variant report

Variant	rs488093
Chromosome Location	chr11:58652029-58652030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58651984-58652034	ProgFib	skin:	n/a
2	chr11:58651984-58652034	BE2_C	brain:	n/a
3	chr11:58651984-58652034	SKMC	muscle:	n/a
4	chr11:58651984-58652034	SK-N-SH_RA	brain:	n/a
5	chr11:58651984-58652034	RPTEC	kidney:	n/a
6	chr11:58651984-58652034	HAEpiC	amniotic membrane:	n/a
7	chr11:58651984-58652034	Hela-S3	cervix:	n/a
8	chr11:58651984-58652034	HCM	heart:	n/a
9	chr11:58651984-58652034	U87	brain:	n/a
10	chr11:58651984-58652034	HNPCEpiC	eye:	n/a
11	chr11:58651984-58652034	AG04449	skin:	fetal
12	chr11:58651984-58652034	PFSK-1	brain:	n/a
13	chr11:58651984-58652034	PrEC	prostate:	n/a
14	chr11:58651984-58652034	HMEC	breast:	n/a
15	chr11:58651984-58652034	HUVEC	blood vessel:	n/a
16	chr11:58651984-58652034	HRPEpiC	eye:	n/a
17	chr11:58651984-58652034	AoSMC	blood vessel:	n/a
18	chr11:58651984-58652034	HEEpiC	esophagus:	n/a
19	chr11:58651984-58652034	PANC-1	pancreas:	n/a
20	chr11:58651984-58652034	NHBE	bronchial:	n/a
21	chr11:58651984-58652034	GM12891	blood:	n/a
22	chr11:58651984-58652034	AG10803	skin:	n/a
23	chr11:58651984-58652034	BJ	skin:	n/a
24	chr11:58651984-58652034	GM12878	blood:	n/a
25	chr11:58651984-58652034	HIPEpiC	eye:	n/a
26	chr11:58651984-58652034	ECC-1	luminal epithelium:	n/a
27	chr11:58651984-58652034	NH-A	brain:	n/a
28	chr11:58651984-58652034	Jurkat	blood:	n/a
29	chr11:58651984-58652034	H1-hESC	embryonic stem cell:	embryo
30	chr11:58651984-58652034	HRE	kidney:	n/a
31	chr11:58651984-58652034	NB4	blood:	n/a
32	chr11:58651984-58652034	SK-N-MC	brain:	n/a
33	chr11:58651984-58652034	A549	lung:	n/a
34	chr11:58651984-58652034	LNCaP	prostate:	n/a
35	chr11:58651984-58652034	GM12892	blood:	n/a
36	chr11:58651984-58652034	HCT-116	colon:	n/a
37	chr11:58651984-58652034	Hepatocyte	liver:	n/a
38	chr11:58651984-58652034	AG09309	skin:	n/a
39	chr11:58651984-58652034	Caco-2	colon:	n/a
40	chr11:58651984-58652034	HepG2	liver:	n/a
41	chr11:58651984-58652034	GM06990	blood:	n/a
42	chr11:58651984-58652034	MCF-7	breast:	n/a
43	chr11:58651984-58652034	NT2-D1	testis:	n/a
44	chr11:58651984-58652034	CMK	blood:	n/a
45	chr11:58651984-58652034	GM19239	blood:	n/a
46	chr11:58651984-58652034	AG09319	gingival:	n/a
47	chr11:58651984-58652034	SK-N-SH	brain:	n/a
48	chr11:58651984-58652034	HPAEpiC	pulmonary alveolar:	n/a
49	chr11:58651984-58652034	HEK293	kidney:	embryo
50	chr11:58651984-58652034	T-47D	breast:	n/a

No data

Variant related genes	Relation type
GLYATL1P2	CpG island

Extended variants
information (count: 134 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10750905	0.89[AFR][1000 genomes]
rs10792188	0.86[AFR][1000 genomes]
rs10792189	0.86[AFR][1000 genomes]
rs10792203	0.88[AFR][1000 genomes]
rs12575251	0.80[EUR][1000 genomes]
rs1943286	0.84[AFR][1000 genomes]
rs1943287	0.86[AFR][1000 genomes]
rs1943288	0.86[AFR][1000 genomes]
rs1943289	0.82[AFR][1000 genomes]
rs1943290	0.86[AFR][1000 genomes]
rs1943291	0.86[AFR][1000 genomes]
rs1943292	0.86[AFR][1000 genomes]
rs1943293	0.86[AFR][1000 genomes]
rs1943294	0.83[AFR][1000 genomes]
rs1943295	0.83[AFR][1000 genomes]
rs1943296	0.83[AFR][1000 genomes]
rs1943297	0.86[AFR][1000 genomes]
rs1943298	0.86[AFR][1000 genomes]
rs1943300	0.88[AFR][1000 genomes]
rs1943301	0.92[AFR][1000 genomes]
rs1943302	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1943306	0.95[AFR][1000 genomes]
rs2156350	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2156351	0.95[AFR][1000 genomes]
rs2187269	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2212850	0.92[AFR][1000 genomes]
rs2226794	0.92[AFR][1000 genomes]
rs2849855	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856259	0.86[AFR][1000 genomes]
rs3020907	0.84[AFR][1000 genomes]
rs3020908	0.86[AFR][1000 genomes]
rs3020909	0.86[AFR][1000 genomes]
rs4103678	0.86[AFR][1000 genomes]
rs490828	0.89[AFR][1000 genomes]
rs492802	0.86[AFR][1000 genomes]
rs493580	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs493659	0.86[AFR][1000 genomes]
rs4939234	0.94[AFR][1000 genomes]
rs4939236	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4939237	0.92[AFR][1000 genomes]
rs4939238	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs496601	0.86[AFR][1000 genomes]
rs497118	0.81[ASN][1000 genomes]
rs497348	0.86[AFR][1000 genomes]
rs512832	0.86[AFR][1000 genomes]
rs513590	0.86[AFR][1000 genomes]
rs518089	0.86[AFR][1000 genomes]
rs519043	0.86[AFR][1000 genomes]
rs519256	0.86[AFR][1000 genomes]
rs519310	0.86[AFR][1000 genomes]
rs521781	0.89[AFR][1000 genomes]
rs524689	0.88[AFR][1000 genomes]
rs526640	0.88[AFR][1000 genomes]
rs529734	0.86[AFR][1000 genomes]
rs531737	0.86[AFR][1000 genomes]
rs533438	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535234	0.86[AFR][1000 genomes]
rs537098	0.85[AFR][1000 genomes]
rs545803	0.86[AFR][1000 genomes]
rs547469	0.86[AFR][1000 genomes]
rs547540	0.95[AFR][1000 genomes]
rs549519	0.94[AFR][1000 genomes]
rs550272	0.83[ASN][1000 genomes]
rs550275	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs552887	0.89[AFR][1000 genomes]
rs557895	0.86[AFR][1000 genomes]
rs558013	0.86[AFR][1000 genomes]
rs558099	0.83[AFR][1000 genomes]
rs558146	0.86[AFR][1000 genomes]
rs558403	0.87[AFR][1000 genomes]
rs560816	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs561676	0.86[AFR][1000 genomes]
rs563687	0.86[AFR][1000 genomes]
rs564570	0.86[AFR][1000 genomes]
rs567460	0.89[AFR][1000 genomes]
rs570835	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs574497	0.82[AFR][1000 genomes]
rs576050	0.86[AFR][1000 genomes]
rs587953	0.86[AFR][1000 genomes]
rs591856	0.89[AFR][1000 genomes]
rs592308	0.89[AFR][1000 genomes]
rs593537	0.81[AFR][1000 genomes]
rs598767	0.86[AFR][1000 genomes]
rs599254	0.86[AFR][1000 genomes]
rs599275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600215	0.86[AFR][1000 genomes]
rs600559	0.89[AFR][1000 genomes]
rs605870	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs608043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs614365	0.86[AFR][1000 genomes]
rs615237	0.86[AFR][1000 genomes]
rs615781	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618527	0.86[ASN][1000 genomes]
rs620633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621584	0.89[AFR][1000 genomes]
rs628312	0.86[AFR][1000 genomes]
rs630551	0.86[AFR][1000 genomes]
rs631452	0.86[AFR][1000 genomes]
rs635588	0.89[AFR][1000 genomes]
rs642957	0.86[AFR][1000 genomes]
rs643881	0.86[AFR][1000 genomes]
rs644238	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs644312	0.86[AFR][1000 genomes]
rs645667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651936	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs657792	0.86[AFR][1000 genomes]
rs658309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6591499	0.81[AMR][1000 genomes]
rs665148	0.89[AFR][1000 genomes]
rs667889	0.88[AFR][1000 genomes]
rs668254	0.88[AFR][1000 genomes]
rs678346	0.86[AFR][1000 genomes]
rs678727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs678880	0.86[AFR][1000 genomes]
rs679551	0.88[AFR][1000 genomes]
rs679625	0.82[ASN][1000 genomes]
rs680053	0.88[AFR][1000 genomes]
rs680976	0.88[AFR][1000 genomes]
rs682357	0.86[AFR][1000 genomes]
rs682780	0.86[AFR][1000 genomes]
rs7116544	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7933339	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription 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	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1048605	chr11:58534660-58672438	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1045858	chr11:58547772-58674568	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
5	nsv1052173	chr11:58553516-58678496	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv508634	chr11:58624088-58657382	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1824025	chr11:58626835-58669877	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1831269	chr11:58626835-58669877	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv528475	chr11:58632368-58656808	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1831555	chr11:58632395-58653147	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58635000-58668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:58645600-58652400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:58648000-58654400	Weak transcription	Fetal Lung	lung
4	chr11:58648000-58655000	Weak transcription	Fetal Intestine Small	intestine
5	chr11:58651000-58671200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:58651400-58660200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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