Variant report

Variant	rs3752515
Chromosome Location	chr1:172539442-172539443
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	chr1:172499376..172501724-chr1:172539037..172541418,2	K562	blood:
2	chr1:172499376..172501667-chr1:172538683..172540537,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10157500	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10157519	0.82[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10218613	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489280	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10752994	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs10798040	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10911856	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912058	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912080	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10912083	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912084	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11805370	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12087284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12121051	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12146100	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1894625	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1894626	0.81[CHB][hapmap]
rs2097492	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2097493	0.87[EUR][1000 genomes]
rs2097494	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2097498	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2157420	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2227188	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2285144	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2422144	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472550	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2472552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2639621	0.82[EUR][1000 genomes]
rs3768444	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4145436	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4433434	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5014539	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6424973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425007	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6656713	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6686080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6695152	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525372	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7531652	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs7539231	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539443	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs763108	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9425646	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9943276	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv872548	chr1:172518012-172551724	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3752515	SUCO	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
3	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
4	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
5	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:172521800-172539800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:172521800-172540400	Strong transcription	Primary B cells from cord blood	blood
8	chr1:172521800-172560400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:172524000-172540400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:172524200-172539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:172524200-172539600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:172524400-172540000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:172524600-172539800	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:172524800-172540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:172525000-172540400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:172526200-172540400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:172527000-172539600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:172527000-172558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:172527200-172540000	Weak transcription	Colonic Mucosa	Colon
20	chr1:172527800-172550400	Weak transcription	Stomach Mucosa	stomach
21	chr1:172527800-172554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:172528400-172543000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:172528400-172547800	Weak transcription	A549	lung
24	chr1:172529200-172539800	Weak transcription	NHLF	lung
25	chr1:172529800-172540000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:172531800-172540400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:172532000-172539600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:172532800-172540400	Strong transcription	Placenta	Placenta
29	chr1:172533000-172540400	Strong transcription	Adipose Nuclei	Adipose
30	chr1:172533200-172540000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:172533200-172540200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:172533400-172540200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:172533400-172540400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr1:172533600-172540000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:172533600-172540000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:172533600-172540200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:172534200-172540000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:172534400-172540400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:172534600-172539800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:172534800-172558000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:172535200-172547800	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:172535200-172558000	Weak transcription	HSMMtube	muscle
43	chr1:172535400-172539600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:172535400-172539800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:172535400-172539800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:172535400-172540200	Weak transcription	Esophagus	oesophagus
47	chr1:172535400-172554200	Weak transcription	NHEK	skin
48	chr1:172535400-172558000	Weak transcription	Left Ventricle	heart
49	chr1:172535400-172558000	Weak transcription	Right Ventricle	heart
50	chr1:172535400-172558200	Weak transcription	Brain Substantia Nigra	brain

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