Variant report

Variant	rs3758802
Chromosome Location	chr11:105480300-105480301
allele	C/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	SMC3	chr11:105479985-105480346	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr11:105480144-105480305	GM12891	blood:	n/a	n/a
3	GATA3	chr11:105479951-105480332	T-47D	breast:	n/a	n/a
4	TEAD4	chr11:105480039-105480354	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr11:105480300-105480450	AG09319	gingival:	n/a	n/a
6	RAD21	chr11:105479958-105480358	H1-hESC	embryonic stem cell:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
7	CTCF	chr11:105480280-105480430	HCM	heart:	n/a	n/a
8	RAD21	chr11:105479976-105481005	H1-hESC	embryonic stem cell:	n/a	chr11:105480199-105480211 chr11:105480242-105480254 chr11:105480886-105480899
9	CTCF	chr11:105480160-105480310	GM12872	blood:	n/a	n/a
10	ATF2	chr11:105479931-105480340	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF2	chr11:105480146-105480328	GM12878	blood:	n/a	n/a
12	CTCF	chr11:105479806-105480456	SK-N-SH	brain:	n/a	n/a
13	ATF2	chr11:105480011-105480374	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr11:105480016-105480348	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3A	chr11:105480043-105481906	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr11:105480002-105480396	ECC-1	luminal epithelium:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
17	RAD21	chr11:105480000-105480338	IMR90	lung:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
18	CTCF	chr11:105480000-105480318	T-47D	breast:	n/a	n/a
19	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
20	RAD21	chr11:105480020-105480319	HepG2	liver:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
21	CTCF	chr11:105479981-105480331	GM12878	blood:	n/a	n/a
22	CTCF	chr11:105480017-105480307	IMR90	lung:	n/a	n/a
23	CTBP2	chr11:105480084-105481474	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr11:105479964-105480350	Hela-S3	cervix:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
25	RAD21	chr11:105479946-105480359	H1-hESC	embryonic stem cell:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
26	RAD21	chr11:105479979-105480321	SK-N-SH_RA	brain:	n/a	chr11:105480199-105480211 chr11:105480242-105480254
27	REST	chr11:105480135-105481694	H1-neurons	neurons:	n/a	chr11:105480767-105480780 chr11:105481187-105481200
28	MXI1	chr11:105479952-105483398	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr11:105480160-105480310	AoAF	blood vessel:	n/a	n/a

Variant related genes	Relation type
GRIA4	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11226791	0.95[ASN][1000 genomes]
rs11226792	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11226804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510168	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2510169	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2510171	0.83[ASN][1000 genomes]
rs2510175	0.89[ASN][1000 genomes]
rs2513254	0.89[ASN][1000 genomes]
rs2513255	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34009389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34548753	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71486022	0.95[ASN][1000 genomes]
rs7482330	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[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:81 , 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	chr11:105479800-105480400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr11:105479800-105480400	Flanking Active TSS	Brain Cingulate Gyrus	brain
5	chr11:105479800-105480600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr11:105479800-105480800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:105479800-105481800	Active TSS	NHDF-Ad	bronchial
8	chr11:105479800-105482000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr11:105479800-105484200	Active TSS	Brain Substantia Nigra	brain
10	chr11:105479800-105488600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr11:105480000-105480400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr11:105480000-105480400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
13	chr11:105480000-105480400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
14	chr11:105480000-105480400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
15	chr11:105480000-105480400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:105480000-105480600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
17	chr11:105480000-105480600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr11:105480000-105480600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:105480000-105480600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:105480000-105480600	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr11:105480000-105480600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr11:105480000-105480800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:105480000-105480800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:105480000-105480800	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr11:105480000-105481000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:105480000-105481200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:105480000-105482000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:105480000-105482000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:105480000-105482200	Active TSS	Fetal Intestine Large	intestine
30	chr11:105480200-105480400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr11:105480200-105480400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:105480200-105480400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
35	chr11:105480200-105480400	Bivalent Enhancer	Liver	Liver
36	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
37	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
38	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
39	chr11:105480200-105480400	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr11:105480200-105480400	Enhancers	Left Ventricle	heart
41	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
42	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
43	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr11:105480200-105480400	Flanking Bivalent TSS/Enh	NHEK	skin
45	chr11:105480200-105480600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:105480200-105480600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:105480200-105480600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
48	chr11:105480200-105480600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:105480200-105480600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:105480200-105480600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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