Variant report

Variant	rs3760372
Chromosome Location	chr17:45380002-45380003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45375988..45378357-chr17:45379217..45383019,3	K562	blood:
2	chr17:45377393..45380597-chr17:45384667..45388953,5	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11079772	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658426	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12600865	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948299	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1969267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271803	1.00[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34589418	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35161461	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35435669	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35983484	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809865	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968314	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4968316	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6504836	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214993	0.86[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7216112	0.87[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs7218813	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221232	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7224753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075410	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9303534	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9893410	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3760372	MRPL45P2	cis	lymphoblastoid	seeQTL
rs3760372	C17orf57	cis	parietal	SCAN
rs3760372	VPS25	cis	cerebellum	SCAN
rs3760372	C17orf57	cis	cerebellum	SCAN
rs3760372	DBF4B	cis	cerebellum	SCAN
rs3760372	KRT31	cis	parietal	SCAN
rs3760372	TBKBP1	cis	lung	GTEx
rs3760372	NBR1	cis	parietal	SCAN
rs3760372	EFTUD2	cis	cerebellum	SCAN
rs3760372	TBKBP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
2	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:45371400-45393000	Weak transcription	Dnd41	blood
4	chr17:45372400-45383600	Weak transcription	Gastric	stomach
5	chr17:45372400-45389600	Weak transcription	Esophagus	oesophagus
6	chr17:45372400-45389800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:45372400-45394400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:45372800-45381400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:45372800-45382800	Weak transcription	Colonic Mucosa	Colon
10	chr17:45373600-45382600	Weak transcription	Spleen	Spleen
11	chr17:45374000-45392800	Weak transcription	Brain Substantia Nigra	brain
12	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr17:45375600-45381600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:45375600-45381800	Strong transcription	Colon Smooth Muscle	Colon
15	chr17:45375800-45381400	Strong transcription	Aorta	Aorta
16	chr17:45375800-45382800	Strong transcription	Fetal Stomach	stomach
17	chr17:45376000-45382600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr17:45376200-45382400	Weak transcription	HSMM	muscle
19	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:45376400-45381800	Strong transcription	Placenta	Placenta
21	chr17:45376800-45381800	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:45377200-45381000	Strong transcription	NHDF-Ad	bronchial
23	chr17:45377200-45381600	Strong transcription	Left Ventricle	heart
24	chr17:45377200-45383400	Weak transcription	Pancreas	Pancrea
25	chr17:45377400-45381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr17:45377600-45381600	Strong transcription	Osteobl	bone
27	chr17:45377800-45380200	Strong transcription	Ovary	ovary
28	chr17:45377800-45380400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:45377800-45381200	Strong transcription	HUVEC	blood vessel
30	chr17:45378200-45381000	Weak transcription	Fetal Intestine Large	intestine
31	chr17:45379000-45382200	Weak transcription	Hela-S3	cervix
32	chr17:45379200-45380200	Strong transcription	Fetal Lung	lung
33	chr17:45379200-45380200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr17:45379200-45380200	ZNF genes & repeats	HSMMtube	muscle
35	chr17:45379200-45380400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:45379200-45382600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:45379400-45380200	ZNF genes & repeats	Brain Hippocampus Middle	brain
38	chr17:45379400-45380200	Strong transcription	Fetal Heart	heart
39	chr17:45379400-45382400	Weak transcription	GM12878-XiMat	blood
40	chr17:45379400-45382600	Weak transcription	K562	blood
41	chr17:45379600-45380200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr17:45379600-45380200	Strong transcription	NHLF	lung
43	chr17:45379600-45381400	Strong transcription	Liver	Liver
44	chr17:45379600-45382600	Strong transcription	Fetal Muscle Leg	muscle
45	chr17:45379600-45390400	Weak transcription	Fetal Intestine Small	intestine
46	chr17:45379800-45380200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:45379800-45380200	Strong transcription	NH-A	brain
48	chr17:45379800-45380400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr17:45379800-45382400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:45379800-45382400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links