Variant report

Variant	rs2472550
Chromosome Location	chr1:172525959-172525960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172501069..172504087-chr1:172524963..172528028,4	MCF-7	breast:
2	chr1:172524779..172527328-chr1:172528773..172530813,3	K562	blood:
3	chr1:172500340..172502764-chr1:172523653..172526492,2	K562	blood:
4	chr1:172524779..172527801-chr1:172528773..172532155,3	K562	blood:
5	chr1:172500883..172502906-chr1:172525690..172527673,2	MCF-7	breast:
6	chr1:172513266..172515531-chr1:172525208..172528046,2	K562	blood:
7	chr1:172518503..172521143-chr1:172524413..172526637,2	K562	blood:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10157500	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10157519	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10218613	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489280	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10752994	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10798040	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10911856	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912058	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912080	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912083	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912084	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11805370	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12087284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121051	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12146100	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894625	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1894626	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2097492	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097493	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2097494	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097498	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2157420	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227188	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285144	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2422144	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472552	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752515	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]
rs3768444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145436	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4433434	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5014539	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425007	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656713	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6686080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695152	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525372	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7531652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7539231	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539443	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763108	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9425646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[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
rs2472550	SUCO	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
2	chr1:172503400-172528600	Weak transcription	Lung	lung
3	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
4	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:172504200-172527000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172506200-172526200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
10	chr1:172507400-172526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:172508200-172526400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:172511800-172528600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:172511800-172557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:172512000-172529000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:172512000-172534200	Weak transcription	Gastric	stomach
18	chr1:172514200-172558800	Weak transcription	Small Intestine	intestine
19	chr1:172514400-172526200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:172514800-172528600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:172514800-172530200	Weak transcription	Thymus	Thymus
22	chr1:172515200-172528000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:172515200-172528200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:172515400-172528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:172516000-172532800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:172516200-172528800	Weak transcription	Pancreas	Pancrea
27	chr1:172516400-172526400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:172516400-172527400	Weak transcription	NHLF	lung
29	chr1:172516600-172528800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:172516800-172550200	Weak transcription	Fetal Heart	heart
31	chr1:172517800-172527200	Weak transcription	Fetal Kidney	kidney
32	chr1:172518000-172529000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:172518600-172533000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:172519000-172530000	Weak transcription	NH-A	brain
35	chr1:172519000-172530200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:172519200-172526800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:172519200-172526800	Weak transcription	A549	lung
38	chr1:172519200-172527200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:172519200-172528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:172519200-172529000	Weak transcription	Brain Germinal Matrix	brain
41	chr1:172519200-172534600	Weak transcription	Right Ventricle	heart
42	chr1:172519200-172559000	Weak transcription	Psoas Muscle	Psoas
43	chr1:172519400-172526400	Weak transcription	Osteobl	bone
44	chr1:172519400-172527600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:172519400-172529000	Weak transcription	NHEK	skin
46	chr1:172519400-172533000	Weak transcription	HUVEC	blood vessel
47	chr1:172519400-172534600	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:172519400-172535400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:172519400-172571600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:172519600-172527400	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links