Variant report

Variant	rs4272720
Chromosome Location	chr10:50263201-50263202
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	chr10:50242711..50245111-chr10:50261545..50265168,4	MCF-7	breast:
2	chr10:50255638..50257367-chr10:50260546..50263382,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10218854	0.82[CHB][hapmap]
rs10508911	0.95[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs10857434	0.95[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs11100985	0.95[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs11100994	0.83[EUR][1000 genomes]
rs11100995	0.86[ASN][1000 genomes]
rs11101001	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11592975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11594275	0.90[ASN][1000 genomes]
rs11594452	0.86[ASN][1000 genomes]
rs11597983	0.86[ASN][1000 genomes]
rs11598768	0.90[ASN][1000 genomes]
rs11814277	1.00[CEU][hapmap]
rs11814668	0.83[EUR][1000 genomes]
rs11815070	0.83[EUR][1000 genomes]
rs11816318	1.00[CEU][hapmap]
rs11817325	1.00[CEU][hapmap]
rs12243520	0.90[ASN][1000 genomes]
rs12780892	0.90[EUR][1000 genomes]
rs17011692	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs17011715	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17011726	1.00[CEU][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes]
rs17011755	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs17011799	0.95[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs17773666	0.95[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs17782866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1806681	1.00[JPT][hapmap]
rs2246796	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2377981	0.86[ASN][1000 genomes]
rs2377982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2377983	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2377984	0.86[ASN][1000 genomes]
rs28505677	0.92[EUR][1000 genomes]
rs36116147	0.98[EUR][1000 genomes]
rs3750744	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4073200	0.86[ASN][1000 genomes]
rs4073201	0.90[ASN][1000 genomes]
rs4073202	0.86[ASN][1000 genomes]
rs41306832	0.86[ASN][1000 genomes]
rs4264085	0.94[EUR][1000 genomes]
rs4284329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4453139	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4838364	0.82[CHB][hapmap]
rs4838445	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs4838455	0.86[ASN][1000 genomes]
rs4838458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs55648711	0.83[EUR][1000 genomes]
rs55687538	0.90[ASN][1000 genomes]
rs55783415	0.83[ASN][1000 genomes]
rs55872223	0.92[EUR][1000 genomes]
rs55890352	0.90[ASN][1000 genomes]
rs55936311	0.83[EUR][1000 genomes]
rs56027486	0.98[EUR][1000 genomes]
rs56157539	0.98[EUR][1000 genomes]
rs56197478	0.92[EUR][1000 genomes]
rs56364323	0.90[ASN][1000 genomes]
rs56737365	0.93[ASN][1000 genomes]
rs57286767	0.90[ASN][1000 genomes]
rs59728475	0.90[ASN][1000 genomes]
rs59889308	0.96[EUR][1000 genomes]
rs61060205	0.90[ASN][1000 genomes]
rs61166027	0.94[EUR][1000 genomes]
rs61848370	0.98[EUR][1000 genomes]
rs61848371	0.98[EUR][1000 genomes]
rs61848377	0.96[EUR][1000 genomes]
rs61848380	0.95[EUR][1000 genomes]
rs61850678	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61850681	0.92[EUR][1000 genomes]
rs61850682	0.95[EUR][1000 genomes]
rs61850684	0.96[EUR][1000 genomes]
rs61850689	0.98[EUR][1000 genomes]
rs61850690	0.98[EUR][1000 genomes]
rs61850693	0.98[EUR][1000 genomes]
rs6537495	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7080670	0.82[CHB][hapmap]
rs7081097	0.90[ASN][1000 genomes]
rs7084861	0.84[EUR][1000 genomes]
rs7088006	0.86[ASN][1000 genomes]
rs7094220	0.82[CHB][hapmap]
rs7094501	0.86[ASN][1000 genomes]
rs7096516	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7097375	0.90[ASN][1000 genomes]
rs72785044	0.90[EUR][1000 genomes]
rs72785050	0.83[EUR][1000 genomes]
rs72785051	0.83[EUR][1000 genomes]
rs72785060	0.85[EUR][1000 genomes]
rs72785072	0.84[EUR][1000 genomes]
rs72785076	0.83[EUR][1000 genomes]
rs72785084	0.82[EUR][1000 genomes]
rs72785087	0.82[EUR][1000 genomes]
rs73302715	0.93[ASN][1000 genomes]
rs73302716	0.93[ASN][1000 genomes]
rs73302780	0.86[ASN][1000 genomes]
rs73302786	0.90[ASN][1000 genomes]
rs7895212	0.83[ASN][1000 genomes]
rs7905715	0.90[CEU][hapmap];0.84[TSI][hapmap]
rs7924204	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[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	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4272720	PTPRU	trans	parietal	SCAN
rs4272720	C10orf128	Cis_1M	lymphoblastoid	RTeQTL
rs4272720	C17orf49	trans	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50222800-50279000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:50232400-50279200	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:50233000-50266000	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:50243800-50278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:50245600-50264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:50247000-50282600	Weak transcription	Brain Angular Gyrus	brain
7	chr10:50247800-50271600	Weak transcription	Fetal Intestine Small	intestine
8	chr10:50254400-50278800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:50255800-50270200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:50257200-50266800	Weak transcription	Aorta	Aorta
11	chr10:50258200-50265800	Weak transcription	Fetal Kidney	kidney
12	chr10:50259200-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:50259800-50264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:50260600-50267800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr10:50261200-50263600	Enhancers	Psoas Muscle	Psoas
16	chr10:50261200-50264800	Genic enhancers	Fetal Stomach	stomach
17	chr10:50261200-50265000	Enhancers	Right Atrium	heart
18	chr10:50261200-50267400	Enhancers	Right Ventricle	heart
19	chr10:50261200-50267600	Enhancers	Left Ventricle	heart
20	chr10:50261200-50267600	Enhancers	Ovary	ovary
21	chr10:50261400-50264200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr10:50261600-50263800	Enhancers	Fetal Lung	lung
23	chr10:50261800-50264600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:50261800-50264600	Weak transcription	Gastric	stomach
25	chr10:50262000-50263800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:50262000-50267600	Genic enhancers	Fetal Muscle Leg	muscle
27	chr10:50262200-50263400	Enhancers	Fetal Brain Male	brain
28	chr10:50262200-50263400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr10:50262400-50263400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr10:50262600-50263800	Weak transcription	Esophagus	oesophagus
31	chr10:50262600-50266400	Weak transcription	HSMMtube	muscle
32	chr10:50262600-50267000	Weak transcription	Lung	lung
33	chr10:50262800-50267400	Enhancers	Adipose Nuclei	Adipose
34	chr10:50262800-50271600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:50263000-50264200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr10:50263000-50264800	Enhancers	NHDF-Ad	bronchial
37	chr10:50263000-50267400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:50263200-50263400	Enhancers	NHLF	lung
39	chr10:50263200-50264400	Weak transcription	Spleen	Spleen
40	chr10:50263200-50264800	Genic enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links