Variant report

Variant	rs443952
Chromosome Location	chr4:76726064-76726065
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	GATA3	chr4:76726021-76726307	SH-SY5Y	brain:	n/a	chr4:76726134-76726150

Variant related genes	Relation type
USO1	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10009902	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10010519	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10014281	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10025315	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10028884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10029110	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11097070	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11729258	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11736474	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13116639	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13118426	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13119659	0.93[ASN][1000 genomes]
rs13133699	0.82[AMR][1000 genomes]
rs13137468	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13138717	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1546539	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1548175	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1553984	1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs1553986	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs186562	0.81[EUR][1000 genomes]
rs1967495	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1967496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs226416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280095	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2869174	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs324682	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324683	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324692	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324707	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324715	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324724	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34385808	0.86[EUR][1000 genomes]
rs3796473	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3796485	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3853183	0.82[CHB][hapmap];0.92[AMR][1000 genomes]
rs3853184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3942252	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4349625	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs436611	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859403	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859542	0.82[AMR][1000 genomes]
rs4859543	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859544	0.82[AMR][1000 genomes]
rs4859545	0.85[AMR][1000 genomes]
rs4859546	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859547	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859548	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859550	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5020591	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6419115	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531841	0.82[EUR][1000 genomes]
rs6531866	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6531867	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6531868	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6531889	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531902	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531903	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67474106	0.84[EUR][1000 genomes]
rs6826858	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6827809	0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6835702	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6835819	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6842216	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855321	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855960	0.84[EUR][1000 genomes]
rs6858741	0.82[AMR][1000 genomes]
rs72651313	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7356270	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7356310	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7657871	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7659408	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7662940	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672378	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7674063	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7674328	0.82[AMR][1000 genomes]
rs7677150	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7685459	0.82[AMR][1000 genomes]
rs7691385	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7691765	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7696241	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7698393	0.89[EUR][1000 genomes]
rs9942164	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
3	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
5	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:76698000-76735400	Weak transcription	Small Intestine	intestine
10	chr4:76705000-76730800	Weak transcription	Fetal Heart	heart
11	chr4:76705800-76730600	Weak transcription	Fetal Brain Female	brain
12	chr4:76706000-76730600	Weak transcription	Aorta	Aorta
13	chr4:76706000-76732000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:76706000-76732000	Weak transcription	Gastric	stomach
15	chr4:76707800-76738600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:76708400-76735400	Weak transcription	Right Ventricle	heart
17	chr4:76710800-76729400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:76711800-76729400	Weak transcription	Fetal Brain Male	brain
19	chr4:76711800-76729400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:76712200-76729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:76712200-76730600	Weak transcription	Brain Angular Gyrus	brain
22	chr4:76712400-76729200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:76712600-76730600	Weak transcription	Brain Germinal Matrix	brain
24	chr4:76712600-76735600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:76713800-76730800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:76715000-76730800	Weak transcription	Pancreas	Pancrea
27	chr4:76715000-76734000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:76715000-76734600	Weak transcription	Esophagus	oesophagus
29	chr4:76716000-76737000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:76718200-76735600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:76720400-76737000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:76720400-76738200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:76720600-76737000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:76720600-76737000	Strong transcription	Osteobl	bone
35	chr4:76720600-76737200	Strong transcription	Liver	Liver
36	chr4:76720800-76728400	Strong transcription	Placenta	Placenta
37	chr4:76720800-76736600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:76720800-76736800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr4:76720800-76737000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:76720800-76737000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr4:76721000-76736400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:76721000-76736600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:76721000-76737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:76721200-76736800	Strong transcription	Fetal Intestine Large	intestine
45	chr4:76721400-76726600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:76721400-76737000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:76721400-76738200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:76721400-76738200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:76721600-76727600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:76721800-76736800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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