Variant report

Variant	rs12769361
Chromosome Location	chr10:50286620-50286621
allele	C/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	GATA3	chr10:50286619-50286704	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
VSTM4	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs12244666	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12244748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12253426	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12255090	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12256777	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12261297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12269023	0.80[CEU][hapmap];0.94[CHB][hapmap]
rs12765281	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12774293	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12776460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011744	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011746	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17700872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17701186	0.88[EUR][1000 genomes]
rs17773851	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2003044	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2137911	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2137912	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2137914	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2246463	0.94[CHB][hapmap]
rs2246673	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246937	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2264846	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2264847	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2490838	0.85[EUR][1000 genomes]
rs2725179	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2725181	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2725184	0.86[EUR][1000 genomes]
rs2725185	0.86[EUR][1000 genomes]
rs2725190	0.85[EUR][1000 genomes]
rs2804937	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs34062275	0.87[EUR][1000 genomes]
rs34110351	0.88[EUR][1000 genomes]
rs34289781	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34364659	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34467986	0.88[EUR][1000 genomes]
rs34574986	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34640094	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34878380	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35341824	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35462783	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35905744	0.88[EUR][1000 genomes]
rs35922675	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924984	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs3924985	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs4073138	0.86[EUR][1000 genomes]
rs4073139	0.87[EUR][1000 genomes]
rs4128908	0.88[CHB][hapmap]
rs4240498	0.94[CHB][hapmap]
rs4364979	0.86[EUR][1000 genomes]
rs4400713	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402204	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4403731	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs4421674	0.94[CHB][hapmap]
rs4445564	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4468264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4481947	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4508127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4550151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4600129	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4644582	0.86[EUR][1000 genomes]
rs55947405	0.86[EUR][1000 genomes]
rs56291725	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58154726	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58893558	0.86[EUR][1000 genomes]
rs6537493	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs6537494	0.94[CHB][hapmap]
rs67269950	0.88[EUR][1000 genomes]
rs68065270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7070387	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7073208	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7074818	0.94[CHB][hapmap]
rs7081243	0.88[EUR][1000 genomes]
rs7084112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7085823	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088718	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7097933	0.80[CEU][hapmap];0.94[CHB][hapmap]
rs7098134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7100655	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs72785015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896344	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7897289	0.89[CHB][hapmap]
rs7904272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7906722	0.88[CHB][hapmap]
rs7907959	0.98[ASN][1000 genomes]
rs7916825	0.89[CHB][hapmap]
rs9804403	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50266600-50289400	Weak transcription	Colonic Mucosa	Colon
2	chr10:50267200-50288400	Weak transcription	NHLF	lung
3	chr10:50272600-50294200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:50273600-50289800	Weak transcription	NHDF-Ad	bronchial
5	chr10:50276600-50288200	Weak transcription	Gastric	stomach
6	chr10:50277600-50287200	Weak transcription	K562	blood
7	chr10:50279600-50289200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:50279800-50288600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:50280600-50288200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:50280600-50288600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:50281600-50288400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:50282400-50289400	Weak transcription	Fetal Kidney	kidney
13	chr10:50283200-50287000	Weak transcription	Lung	lung
14	chr10:50283200-50288600	Weak transcription	Placenta	Placenta
15	chr10:50283200-50298200	Weak transcription	Spleen	Spleen
16	chr10:50284000-50288600	Weak transcription	Esophagus	oesophagus
17	chr10:50284200-50288200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:50284600-50288400	Weak transcription	Aorta	Aorta
19	chr10:50284600-50288600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:50284800-50287400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:50284800-50288200	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:50284800-50292400	Enhancers	Liver	Liver
23	chr10:50285000-50286800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:50285000-50287000	Weak transcription	Fetal Intestine Small	intestine
25	chr10:50285200-50287600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:50285200-50288200	Weak transcription	Left Ventricle	heart
27	chr10:50285200-50292400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr10:50285400-50286800	Enhancers	HSMMtube	muscle
29	chr10:50285400-50288200	Weak transcription	Brain Angular Gyrus	brain
30	chr10:50285400-50288200	Weak transcription	Fetal Stomach	stomach
31	chr10:50285400-50288200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr10:50285400-50288400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:50285400-50288400	Weak transcription	Pancreas	Pancrea
34	chr10:50285400-50289200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:50285400-50289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:50285600-50286800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr10:50285600-50287200	Weak transcription	Adipose Nuclei	Adipose
38	chr10:50285600-50287200	Weak transcription	Fetal Lung	lung
39	chr10:50285600-50288200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:50285600-50288200	Weak transcription	Fetal Muscle Leg	muscle
41	chr10:50285600-50288200	Weak transcription	Fetal Thymus	thymus
42	chr10:50285600-50288200	Weak transcription	Right Atrium	heart
43	chr10:50285600-50288400	Weak transcription	Brain Anterior Caudate	brain
44	chr10:50285600-50288400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr10:50285600-50288400	Weak transcription	Brain Hippocampus Middle	brain
46	chr10:50285600-50288600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:50286000-50287200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr10:50286000-50292400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:50286200-50287200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:50286400-50287200	Weak transcription	Brain Substantia Nigra	brain

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