Variant report

Variant	rs13072690
Chromosome Location	chr3:135769410-135769411
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	GATA2	chr3:135768747-135769447	SH-SY5Y	brain:	n/a	chr3:135768979-135768989

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135767256..135769755-chr3:135772034..135773632,2	K562	blood:

Variant related genes	Relation type
ENSG00000227267	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12630389	0.81[ASN][1000 genomes]
rs12632791	0.85[ASN][1000 genomes]
rs12633805	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12637541	0.83[ASN][1000 genomes]
rs13059064	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065499	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13069408	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072433	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13072782	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]
rs13075579	0.87[ASN][1000 genomes]
rs13078865	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079037	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13084404	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13092707	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13097172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097176	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097267	0.88[ASN][1000 genomes]
rs13100235	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523593	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1523598	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1523599	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1523600	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs16843560	0.82[ASN][1000 genomes]
rs16843611	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2140450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177407	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2400649	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447526	0.88[ASN][1000 genomes]
rs35097316	0.83[ASN][1000 genomes]
rs35532770	0.87[ASN][1000 genomes]
rs35946332	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961065	0.85[ASN][1000 genomes]
rs3946444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075999	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4331626	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4678224	0.86[ASN][1000 genomes]
rs4678288	0.88[ASN][1000 genomes]
rs4678432	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678434	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4678435	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs55873361	0.88[ASN][1000 genomes]
rs56152207	0.88[ASN][1000 genomes]
rs57594457	0.88[ASN][1000 genomes]
rs60070757	0.88[ASN][1000 genomes]
rs61791712	0.88[ASN][1000 genomes]
rs61791714	0.88[ASN][1000 genomes]
rs6439603	0.82[ASN][1000 genomes]
rs6439605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439609	0.83[ASN][1000 genomes]
rs6439610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439614	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439615	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439618	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439622	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439623	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439624	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs6770366	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771950	0.88[ASN][1000 genomes]
rs6775261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779903	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6793273	0.80[ASN][1000 genomes]
rs6803786	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7433592	0.88[ASN][1000 genomes]
rs7610302	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625607	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635621	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650079	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9289501	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs940229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9758578	0.89[ASN][1000 genomes]
rs9846554	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856799	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9868239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:135742800-135774200	Weak transcription	HMEC	breast
3	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:135750400-135772800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:135750800-135775800	Weak transcription	Liver	Liver
6	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:135758200-135771200	Weak transcription	Stomach Mucosa	stomach
8	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:135761600-135783400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:135762200-135772800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:135762200-135773000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:135762200-135774000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:135762400-135771400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:135763000-135785600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:135763200-135770000	Strong transcription	Fetal Intestine Large	intestine
16	chr3:135763200-135772600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:135763200-135775000	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:135763200-135776800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:135763600-135775600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:135763800-135770000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:135764400-135771200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:135764400-135771200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:135764600-135771000	Weak transcription	Lung	lung
25	chr3:135764600-135772200	Weak transcription	Colonic Mucosa	Colon
26	chr3:135764600-135773800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:135764600-135774400	Weak transcription	NHEK	skin
28	chr3:135764600-135778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:135764800-135769600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:135764800-135775800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:135765000-135774200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:135765000-135776400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:135765000-135777800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:135765000-135781000	Weak transcription	Fetal Brain Female	brain
36	chr3:135765000-135781200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:135765000-135781200	Weak transcription	Fetal Intestine Small	intestine
38	chr3:135765000-135786000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
40	chr3:135765400-135777600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:135765600-135771000	Weak transcription	Right Ventricle	heart
42	chr3:135765600-135772200	Weak transcription	NH-A	brain
43	chr3:135765600-135784200	Weak transcription	Fetal Kidney	kidney
44	chr3:135765600-135785400	Weak transcription	Pancreas	Pancrea
45	chr3:135766800-135769800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:135767000-135772600	Strong transcription	Ovary	ovary
47	chr3:135767000-135772600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:135767000-135775000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr3:135767200-135774400	Weak transcription	Fetal Brain Male	brain
50	chr3:135767600-135769600	Strong transcription	NHLF	lung

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