Variant report

Variant	rs3762593
Chromosome Location	chr2:98429438-98429439
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98428768..98431337-chr2:98613628..98615730,2	K562	blood:
2	chr2:98427986..98429941-chr2:98431797..98434605,2	K562	blood:
3	chr2:98427579..98430220-chr2:98610918..98612535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10176201	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10182941	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10200949	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10211231	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1071885	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865055	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11123924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123949	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123966	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11690482	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11693874	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11888323	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11899171	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712123	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712174	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13003978	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13006817	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13008503	0.82[ASN][1000 genomes]
rs13010946	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13022778	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13034644	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1317178	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13405546	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1466924	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1503200	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1922280	0.90[ASN][1000 genomes]
rs1922282	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017028	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2091772	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2100058	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2141862	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279826	0.80[ASN][1000 genomes]
rs2309316	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309317	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2309356	0.83[ASN][1000 genomes]
rs4274643	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4560167	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5865	0.92[ASN][1000 genomes]
rs6543108	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543109	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543161	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543177	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543202	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543210	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709571	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710813	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723466	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6723653	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6744331	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748809	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6748927	0.98[ASN][1000 genomes]
rs7558931	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7561104	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562695	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567397	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574437	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577886	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582664	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586210	0.80[ASN][1000 genomes]
rs7598116	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7602412	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7605180	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs930607	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308862	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs956696	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9973416	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3762593	ZAP70	cis	Nerve Tibial	GTEx
rs3762593	ACHE	trans	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98387800-98438200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:98399600-98429600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:98402000-98440400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:98405800-98459600	Weak transcription	Stomach Mucosa	stomach
5	chr2:98406400-98469200	Weak transcription	A549	lung
6	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
7	chr2:98409600-98429800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
9	chr2:98410000-98435800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:98410000-98446000	Weak transcription	Colonic Mucosa	Colon
11	chr2:98410000-98456200	Weak transcription	Thymus	Thymus
12	chr2:98410000-98456800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:98410000-98456800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:98410000-98457400	Weak transcription	Small Intestine	intestine
15	chr2:98410800-98432000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:98422000-98436200	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:98422000-98456200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:98423400-98431000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr2:98423600-98430800	Strong transcription	Fetal Thymus	thymus
20	chr2:98423800-98429600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:98423800-98437200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:98424000-98430800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:98424000-98438600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:98424000-98442600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:98424000-98446800	Weak transcription	Fetal Heart	heart
26	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:98424200-98429800	Strong transcription	Primary T cells from cord blood	blood
28	chr2:98424200-98432000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:98424400-98430800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:98424400-98431000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:98424400-98431000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:98424600-98430800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:98424600-98430800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:98424600-98431000	Strong transcription	Placenta	Placenta
36	chr2:98424600-98431200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:98424600-98432200	Strong transcription	Liver	Liver
38	chr2:98424800-98430800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr2:98424800-98430800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:98424800-98430800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:98424800-98430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:98424800-98430800	Strong transcription	Dnd41	blood
43	chr2:98424800-98431000	Strong transcription	Adipose Nuclei	Adipose
44	chr2:98424800-98431000	Strong transcription	Fetal Intestine Large	intestine
45	chr2:98424800-98432200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:98424800-98432800	Strong transcription	HepG2	liver
47	chr2:98424800-98436600	Strong transcription	Primary B cells from cord blood	blood
48	chr2:98425000-98429800	Strong transcription	Left Ventricle	heart
49	chr2:98425000-98430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:98425000-98431000	Strong transcription	GM12878-XiMat	blood

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