Variant report

Variant	rs4939228
Chromosome Location	chr11:58612825-58612826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:58612700-58613192	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr11:58612773-58613283	SH-SY5Y	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58612814-58612864	HRPEpiC	eye:	n/a
2	chr11:58612814-58612864	IMR90	lung:	fetal
3	chr11:58612814-58612864	SK-N-MC	brain:	n/a
4	chr11:58612814-58612864	RPTEC	kidney:	n/a
5	chr11:58612814-58612864	Jurkat	blood:	n/a
6	chr11:58612814-58612864	H1-hESC	embryonic stem cell:	embryo
7	chr11:58612814-58612864	ECC-1	luminal epithelium:	n/a
8	chr11:58612814-58612864	NHBE	bronchial:	n/a
9	chr11:58612814-58612864	NH-A	brain:	n/a
10	chr11:58612814-58612864	HRCEpiC	kidney:	n/a
11	chr11:58612814-58612864	AG09309	skin:	n/a
12	chr11:58612814-58612864	HL-60	blood:	n/a
13	chr11:58612814-58612864	HNPCEpiC	eye:	n/a
14	chr11:58612814-58612864	HUVEC	blood vessel:	n/a
15	chr11:58612814-58612864	MCF-7	breast:	n/a
16	chr11:58612814-58612864	Hepatocyte	liver:	n/a
17	chr11:58612814-58612864	SKMC	muscle:	n/a
18	chr11:58612814-58612864	AoSMC	blood vessel:	n/a
19	chr11:58612814-58612864	HEK293	kidney:	embryo
20	chr11:58612814-58612864	HCT-116	colon:	n/a
21	chr11:58612814-58612864	NHDF-neo	bronchial:	n/a
22	chr11:58612814-58612864	HEEpiC	esophagus:	n/a
23	chr11:58612814-58612864	LNCaP	prostate:	n/a
24	chr11:58612814-58612864	AG04450	lung:	fetal
25	chr11:58612814-58612864	PANC-1	pancreas:	n/a
26	chr11:58612814-58612864	GM19239	blood:	n/a
27	chr11:58612814-58612864	GM06990	blood:	n/a
28	chr11:58612814-58612864	HIPEpiC	eye:	n/a
29	chr11:58612814-58612864	T-47D	breast:	n/a
30	chr11:58612814-58612864	HRE	kidney:	n/a
31	chr11:58612814-58612864	BJ	skin:	n/a
32	chr11:58612814-58612864	HepG2	liver:	n/a
33	chr11:58612814-58612864	BE2_C	brain:	n/a
34	chr11:58612814-58612864	AG04449	skin:	fetal
35	chr11:58612814-58612864	SK-N-SH_RA	brain:	n/a
36	chr11:58612814-58612864	Caco-2	colon:	n/a
37	chr11:58612814-58612864	GM12892	blood:	n/a
38	chr11:58612814-58612864	HPAEpiC	pulmonary alveolar:	n/a
39	chr11:58612814-58612864	A549	lung:	n/a
40	chr11:58612814-58612864	AG10803	skin:	n/a
41	chr11:58612814-58612864	CMK	blood:	n/a
42	chr11:58612814-58612864	HCM	heart:	n/a
43	chr11:58612814-58612864	MCF10A-Er-Src	breast:	n/a
44	chr11:58612814-58612864	SAEC	small airway:	n/a
45	chr11:58612814-58612864	PrEC	prostate:	n/a
46	chr11:58612814-58612864	HMEC	breast:	n/a
47	chr11:58612814-58612864	NB4	blood:	n/a
48	chr11:58612814-58612864	AG09319	gingival:	n/a
49	chr11:58612814-58612864	U87	brain:	n/a
50	chr11:58612814-58612864	GM12878	blood:	n/a

No data

Variant related genes	Relation type
GLYATL2	TF binding region
GLYATL2	CpG island

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1014068	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792181	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10792183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792185	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896825	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10896828	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10896830	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10896832	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10896845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896847	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896848	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896849	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896852	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896854	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896857	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896859	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229625	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11229626	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11229629	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11229648	0.81[ASN][1000 genomes]
rs11229649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229650	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229651	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229653	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229655	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229656	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229657	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229661	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11535770	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12146504	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12146511	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12223073	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12224097	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12224475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893631	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893632	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938701	0.88[AMR][1000 genomes]
rs1938708	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1938709	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1938711	0.84[ASN][1000 genomes]
rs1938714	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1938715	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1938716	0.83[ASN][1000 genomes]
rs1943254	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943258	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943262	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943263	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943267	0.82[AMR][1000 genomes]
rs1943268	0.82[AMR][1000 genomes]
rs1943271	0.85[AMR][1000 genomes]
rs1943272	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1943276	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1943280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1943281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1943282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1943303	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943307	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1943308	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1962553	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2097018	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097019	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2156346	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2186414	0.82[AMR][1000 genomes]
rs2187264	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2212845	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2497368	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2497372	0.88[AMR][1000 genomes]
rs2497376	0.88[AMR][1000 genomes]
rs2497379	0.88[AMR][1000 genomes]
rs34366794	0.81[ASN][1000 genomes]
rs4939220	0.84[ASN][1000 genomes]
rs4939222	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4939226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4939227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939229	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939230	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507224	0.88[AMR][1000 genomes]
rs547178	0.88[AMR][1000 genomes]
rs547895	0.88[AMR][1000 genomes]
rs56383501	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56407726	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570146	0.88[AMR][1000 genomes]
rs570244	0.88[AMR][1000 genomes]
rs572006	0.85[AMR][1000 genomes]
rs58504618	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591121	0.88[AMR][1000 genomes]
rs621137	0.88[AMR][1000 genomes]
rs667445	0.88[AMR][1000 genomes]
rs7104137	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7115145	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119206	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72913216	0.81[AFR][1000 genomes]
rs72929706	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72929752	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888240	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9943656	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv523481	chr11:58553771-58632368	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv525355	chr11:58553771-58632368	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv1827788	chr11:58595883-58636405	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58610800-58614200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr11:58610800-58614600	Enhancers	Primary hematopoietic stem cells	blood
3	chr11:58611600-58613200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr11:58611600-58613400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:58611800-58613200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:58612400-58613000	Enhancers	Primary B cells from peripheral blood	blood
7	chr11:58612800-58613000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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