Variant report

Variant	rs13269925
Chromosome Location	chr8:61431991-61431992
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	CHD1	chr8:61431989-61432083	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr8:61428909-61432038	HepG2	liver:	n/a	n/a
3	WRNIP1	chr8:61431587-61432015	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251396	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10091703	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10100740	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10101576	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10101714	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10103438	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10109278	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10110436	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014860	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10435602	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10504311	0.81[ASN][1000 genomes]
rs10957135	0.81[ASN][1000 genomes]
rs10957136	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10957137	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10957138	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957140	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957141	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957143	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957146	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957149	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11774500	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775407	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11778529	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778708	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778772	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778888	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11782178	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11782463	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784284	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11786146	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11988528	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12678694	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12680436	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12681841	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13266707	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13267765	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13267828	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480342	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2326556	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2326557	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2625445	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28405386	0.82[ASN][1000 genomes]
rs28495747	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542403	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28678079	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875966	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34234629	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34523017	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34775344	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35837434	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35853087	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592014	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602724	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603239	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610455	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624407	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471884	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649634	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664796	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66983460	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs671275	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs677467	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684573	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6987523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991529	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6993237	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6996344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6998294	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7017556	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7357376	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7462738	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7812421	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7820349	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822391	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826226	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7832664	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7832964	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7842105	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9437	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643524	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv971314	chr8:61359401-61436209	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13269925	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61428600-61432000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr8:61428600-61432000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:61428600-61432400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:61428600-61434400	Active TSS	GM12878-XiMat	blood
5	chr8:61428800-61432000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:61428800-61432000	Active TSS	Left Ventricle	heart
7	chr8:61428800-61432000	Active TSS	Lung	lung
8	chr8:61428800-61432200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr8:61428800-61432200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:61428800-61432400	Active TSS	HSMMtube	muscle
11	chr8:61428800-61432600	Active TSS	Right Ventricle	heart
12	chr8:61428800-61433200	Active TSS	Right Atrium	heart
13	chr8:61429000-61432000	Active TSS	Pancreas	Pancrea
14	chr8:61429000-61432200	Active TSS	Fetal Intestine Large	intestine
15	chr8:61430000-61432000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr8:61430200-61432000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr8:61430200-61432000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr8:61430200-61432400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr8:61430400-61432000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr8:61430400-61432000	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr8:61430400-61432000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr8:61430400-61432200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:61430400-61432200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:61430400-61432600	Flanking Active TSS	Fetal Brain Female	brain
25	chr8:61430400-61432800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr8:61430600-61432000	Flanking Active TSS	Liver	Liver
27	chr8:61430600-61432000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr8:61430600-61432200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr8:61430600-61432400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:61430600-61432400	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr8:61430600-61433400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr8:61430800-61432000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr8:61430800-61432000	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr8:61430800-61432000	Flanking Active TSS	Thymus	Thymus
35	chr8:61430800-61432200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr8:61430800-61432200	Flanking Active TSS	Fetal Lung	lung
37	chr8:61430800-61432200	Flanking Active TSS	NHEK	skin
38	chr8:61430800-61432600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:61430800-61432600	Flanking Active TSS	Dnd41	blood
40	chr8:61430800-61433000	Flanking Active TSS	HUVEC	blood vessel
41	chr8:61430800-61433200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr8:61431000-61432000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr8:61431000-61432000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr8:61431000-61432000	Enhancers	Fetal Thymus	thymus
45	chr8:61431000-61432000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr8:61431000-61432200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr8:61431000-61432200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr8:61431000-61432600	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr8:61431000-61432800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:61431000-61433400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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