Variant report

Variant	rs3758799
Chromosome Location	chr11:105481213-105481214
allele	A/G
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	GTF2F1	chr11:105481179-105481322	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr11:105481210-105481599	SK-N-SH_RA	brain:	n/a	chr11:105481314-105481323 chr11:105481312-105481323 chr11:105481427-105481449
3	POLR2A	chr11:105480937-105481569	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr11:105481154-105481601	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr11:105481200-105481470	HRE	kidney:	n/a	n/a
6	CHD1	chr11:105481158-105482296	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:105481018-105481532	H1-neurons	neurons:	n/a	n/a
8	MAX	chr11:105481204-105481535	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr11:105481012-105481599	H1-hESC	embryonic stem cell:	n/a	n/a
10	GATA2	chr11:105480684-105482031	SH-SY5Y	brain:	n/a	chr11:105481881-105481897
11	POLR2A	chr11:105481119-105481490	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr11:105480986-105481630	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr11:105481002-105481564	H1-hESC	embryonic stem cell:	n/a	chr11:105481494-105481501 chr11:105481494-105481501 chr11:105481493-105481501 chr11:105481494-105481501
14	TBP	chr11:105480666-105481489	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr11:105480991-105481748	H1-hESC	embryonic stem cell:	n/a	chr11:105481494-105481501 chr11:105481494-105481501 chr11:105481626-105481640 chr11:105481493-105481501 chr11:105481494-105481501
16	SIN3A	chr11:105480043-105481906	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr11:105481154-105481558	SK-N-SH_RA	brain:	n/a	chr11:105481413-105481420 chr11:105481235-105481247
18	JUND	chr11:105480564-105481982	H1-hESC	embryonic stem cell:	n/a	n/a
19	TAF1	chr11:105480622-105481621	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr11:105481173-105481563	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr11:105480465-105481700	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOXP2	chr11:105481128-105481497	PFSK-1	brain:	n/a	n/a
23	RAD21	chr11:105479744-105482923	SK-N-SH	brain:	n/a	chr11:105481413-105481420 chr11:105480199-105480211 chr11:105480242-105480254 chr11:105480886-105480899 chr11:105481235-105481247 chr11:105482690-105482703
24	POLR2A	chr11:105481029-105483298	H1-neurons	neurons:	n/a	n/a
25	ZNF143	chr11:105480621-105481431	H1-hESC	embryonic stem cell:	n/a	chr11:105481267-105481285
26	YY1	chr11:105480451-105481610	H1-hESC	embryonic stem cell:	n/a	chr11:105481314-105481323 chr11:105480885-105480896 chr11:105481312-105481323 chr11:105481427-105481449
27	YY1	chr11:105481211-105481571	SK-N-SH_RA	brain:	n/a	chr11:105481314-105481323 chr11:105481312-105481323 chr11:105481427-105481449
28	CTBP2	chr11:105480084-105481474	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr11:105481065-105481556	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr11:105481112-105481492	H1-hESC	embryonic stem cell:	n/a	chr11:105481314-105481323 chr11:105481312-105481323 chr11:105481427-105481449
31	REST	chr11:105480135-105481694	H1-neurons	neurons:	n/a	chr11:105480767-105480780 chr11:105481187-105481200
32	MXI1	chr11:105479952-105483398	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
GRIA4	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11226809	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12099383	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562221	0.85[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59835889	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60839987	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66955071	1.00[ASN][1000 genomes]
rs67083862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68185149	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110163	0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114503	0.88[EUR][1000 genomes]
rs7115187	0.86[EUR][1000 genomes]
rs72988133	0.80[ASN][1000 genomes]
rs72988181	1.00[ASN][1000 genomes]
rs72991703	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949337	chr11:104950007-105510193	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105479200-105484400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr11:105479400-105485800	Active TSS	Brain Angular Gyrus	brain
3	chr11:105479800-105481800	Active TSS	NHDF-Ad	bronchial
4	chr11:105479800-105482000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:105479800-105484200	Active TSS	Brain Substantia Nigra	brain
6	chr11:105479800-105488600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr11:105480000-105482000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:105480000-105482000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:105480000-105482200	Active TSS	Fetal Intestine Large	intestine
10	chr11:105480200-105481400	Enhancers	Esophagus	oesophagus
11	chr11:105480200-105481600	Active TSS	Rectal Smooth Muscle	rectum
12	chr11:105480200-105482000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr11:105480200-105482000	Enhancers	Spleen	Spleen
14	chr11:105480200-105482200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:105480200-105482200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
16	chr11:105480200-105482400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:105480200-105482400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:105480200-105482600	Active TSS	Fetal Brain Male	brain
19	chr11:105480200-105482800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr11:105480200-105483000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:105480200-105483000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:105480400-105481800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr11:105480400-105482600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr11:105480400-105482600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:105480400-105482600	Active TSS	Brain Cingulate Gyrus	brain
26	chr11:105480400-105482800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
27	chr11:105480400-105483200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr11:105480400-105483200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:105480400-105484000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr11:105480400-105484200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:105480600-105481400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr11:105480600-105481600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:105480600-105481800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr11:105480600-105481800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr11:105480600-105482000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr11:105480600-105482000	Active TSS	Right Ventricle	heart
37	chr11:105480600-105482400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr11:105480600-105482400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr11:105480600-105482400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr11:105480600-105482400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr11:105480600-105482600	Active TSS	Brain Germinal Matrix	brain
42	chr11:105480600-105484000	Active TSS	Brain Anterior Caudate	brain
43	chr11:105480600-105485400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:105480800-105481400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:105480800-105481400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:105480800-105481400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
47	chr11:105480800-105481400	Flanking Active TSS	Pancreas	Pancrea
48	chr11:105480800-105481600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:105480800-105481600	Active TSS	Aorta	Aorta
50	chr11:105480800-105481800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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