Variant report

Variant	rs3924768
Chromosome Location	chr1:213401648-213401649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213398206..213399824-chr1:213400254..213403219,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10779599	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864037	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10864039	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120082	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11120084	0.81[AMR][1000 genomes]
rs11120100	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120102	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120104	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12144379	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12401550	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498355	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359554	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34691780	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34868056	0.88[AMR][1000 genomes]
rs4393210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951664	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951676	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60968477	0.85[AMR][1000 genomes]
rs6540777	0.81[AMR][1000 genomes]
rs6670496	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671019	0.83[AMR][1000 genomes]
rs6697921	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7517229	0.85[ASN][1000 genomes]
rs7547782	0.81[ASN][1000 genomes]
rs9645358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9728406	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1012014	chr1:213371127-213423214	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001201	chr1:213385827-213428021	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3924768	ANGEL2	cis	parietal	SCAN
rs3924768	ANGEL2	cis	cerebellum	SCAN
rs3924768	ANGEL2	cis	Nerve Tibial	GTEx
rs3924768	RPS6KC1	cis	Artery Tibial	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213326600-213422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:213340600-213424600	Weak transcription	Pancreas	Pancrea
3	chr1:213345600-213404600	Weak transcription	Osteobl	bone
4	chr1:213360400-213405200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:213362200-213415400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:213370800-213427600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:213372000-213405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:213372600-213413800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:213372800-213414000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:213373000-213405200	Weak transcription	Left Ventricle	heart
11	chr1:213373000-213414200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:213373000-213423000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:213373200-213405000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:213373200-213417000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:213375800-213405200	Weak transcription	Psoas Muscle	Psoas
16	chr1:213375800-213405200	Weak transcription	HSMM	muscle
17	chr1:213376800-213414200	Weak transcription	Brain Anterior Caudate	brain
18	chr1:213378800-213405200	Weak transcription	K562	blood
19	chr1:213378800-213421200	Weak transcription	Fetal Kidney	kidney
20	chr1:213379000-213405200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:213381600-213425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:213382600-213405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:213385600-213407000	Weak transcription	Stomach Mucosa	stomach
24	chr1:213386000-213405400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:213386600-213404800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:213387400-213414000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:213387600-213405000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:213388000-213405200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:213388000-213405200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:213388000-213414400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:213388000-213424600	Weak transcription	Gastric	stomach
32	chr1:213388200-213414000	Weak transcription	Aorta	Aorta
33	chr1:213388200-213414000	Weak transcription	Liver	Liver
34	chr1:213388200-213414200	Weak transcription	Ovary	ovary
35	chr1:213388200-213417200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:213388200-213426200	Weak transcription	Lung	lung
37	chr1:213388200-213455400	Weak transcription	Placenta	Placenta
38	chr1:213388400-213402200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:213388400-213404400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:213388400-213404600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:213388400-213405200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:213388400-213405200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:213388400-213405400	Weak transcription	Adipose Nuclei	Adipose
44	chr1:213388400-213407400	Weak transcription	Fetal Stomach	stomach
45	chr1:213388400-213407600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:213388400-213414000	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:213388400-213414200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:213388400-213414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:213388400-213414200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:213388600-213402800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links