Variant report

Variant	rs61892604
Chromosome Location	chr11:58672544-58672545
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	TAF1	chr11:58672539-58673636	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr11:58671256-58673866	HEK293-T-REx	kidney:	n/a	chr11:58671955-58671976 chr11:58671880-58671889
3	RCOR1	chr11:58672269-58673181	IMR90	lung:	n/a	n/a
4	MAX	chr11:58672506-58673760	SK-N-SH	brain:	n/a	chr11:58673548-58673559
5	CTCF	chr11:58672440-58672590	HA-sp	spinal cord:	n/a	n/a
6	CHD1	chr11:58672403-58673216	IMR90	lung:	n/a	n/a
7	MAX	chr11:58672483-58673931	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
8	KAP1	chr11:58672432-58673114	HEK293	kidney:	n/a	n/a
9	E2F6	chr11:58672534-58674084	H1-hESC	embryonic stem cell:	n/a	chr11:58673476-58673483 chr11:58673476-58673483 chr11:58673272-58673281 chr11:58673472-58673484 chr11:58673476-58673483 chr11:58673475-58673484
10	SIN3A	chr11:58672415-58673795	H1-hESC	embryonic stem cell:	n/a	chr11:58673223-58673234
11	MXI1	chr11:58672155-58674226	SK-N-SH	brain:	n/a	n/a
12	MAX	chr11:58672477-58673886	H1-hESC	embryonic stem cell:	n/a	chr11:58673548-58673559
13	POLR2A	chr11:58672544-58673353	ProgFib	skin:	n/a	n/a
14	POLR2A	chr11:58672473-58673794	H1-hESC	embryonic stem cell:	n/a	n/a
15	KAP1	chr11:58672489-58672992	U2OS	brain:	n/a	n/a
16	TAF1	chr11:58672460-58673168	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr11:58672420-58672570	AG09319	gingival:	n/a	n/a
18	REST	chr11:58672357-58673922	H1-neurons	neurons:	n/a	chr11:58672832-58672852 chr11:58672763-58672776 chr11:58672833-58672851 chr11:58672832-58672852
19	CTCF	chr11:58672540-58672690	AoAF	blood vessel:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYATL1-3	chr11:58672343-58672709	NONHSAT021486

Variant related genes	Relation type
GLYATL2	TF binding region
ENSG00000224130	TF binding region
GLYATL1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10792206	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896872	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896873	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896874	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896875	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896877	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896878	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896879	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896880	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896882	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896883	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896884	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229689	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229692	0.83[ASN][1000 genomes]
rs11229693	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229694	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229695	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229701	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229704	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229705	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229708	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229711	0.96[ASN][1000 genomes]
rs12222597	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12272494	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12277628	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12278662	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12281983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12292314	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1808064	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1815856	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1893627	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893628	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893629	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938786	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1943264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2156344	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2156345	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2156349	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740950	0.81[ASN][1000 genomes]
rs4271397	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4547111	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4573693	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939243	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56155456	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58848038	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61889804	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61889805	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7108461	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118637	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7126489	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7129011	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73483072	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7939049	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948818	0.84[ASN][1000 genomes]
rs948819	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787921	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	esv3502182	chr11:58668199-58731237	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3502181	chr11:58668236-58731215	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3478019	chr11:58668282-58731214	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3478030	chr11:58668282-58731214	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3502183	chr11:58668353-58731177	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58668800-58672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:58668800-58672600	Weak transcription	Pancreas	Pancrea
3	chr11:58671200-58673400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:58671200-58673800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:58671200-58673800	Active TSS	NHLF	lung
6	chr11:58671400-58673000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr11:58671400-58673600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:58671400-58673800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:58671400-58673800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr11:58671600-58672600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr11:58671600-58673200	Flanking Active TSS	HMEC	breast
12	chr11:58671800-58672600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr11:58671800-58672800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:58671800-58672800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr11:58671800-58673400	Active TSS	NH-A	brain
16	chr11:58672000-58672600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
17	chr11:58672000-58672600	Active TSS	Fetal Muscle Leg	muscle
18	chr11:58672000-58673600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr11:58672000-58673600	Active TSS	Fetal Brain Female	brain
20	chr11:58672000-58673600	Active TSS	NHDF-Ad	bronchial
21	chr11:58672200-58672600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
22	chr11:58672200-58672600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
23	chr11:58672200-58673200	Bivalent/Poised TSS	Fetal Stomach	stomach
24	chr11:58672200-58673400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr11:58672200-58673600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr11:58672200-58673600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:58672200-58673600	Active TSS	Fetal Brain Male	brain
28	chr11:58672200-58674000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr11:58672400-58672600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:58672400-58672600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:58672400-58672600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:58672400-58672600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:58672400-58672600	Active TSS	Brain Angular Gyrus	brain
34	chr11:58672400-58672600	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr11:58672400-58672600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr11:58672400-58672600	Active TSS	Fetal Muscle Trunk	muscle
37	chr11:58672400-58672600	Enhancers	HSMMtube	muscle
38	chr11:58672400-58672800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr11:58672400-58672800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:58672400-58672800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr11:58672400-58672800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:58672400-58672800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:58672400-58672800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr11:58672400-58672800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr11:58672400-58672800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr11:58672400-58672800	Bivalent/Poised TSS	Fetal Lung	lung
47	chr11:58672400-58673000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:58672400-58673000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:58672400-58673000	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr11:58672400-58673000	Flanking Active TSS	NHEK	skin

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