Variant report

Variant	rs7709645
Chromosome Location	chr5:60731458-60731459
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10041978	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1045352	0.80[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs10939900	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10939901	0.99[ASN][1000 genomes]
rs10939902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939903	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11743711	0.89[ASN][1000 genomes]
rs11749200	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11750589	0.98[ASN][1000 genomes]
rs11950318	0.86[ASN][1000 genomes]
rs11952146	0.80[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs11954430	0.81[ASN][1000 genomes]
rs11954859	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12187112	0.95[ASN][1000 genomes]
rs12188627	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12189001	0.99[ASN][1000 genomes]
rs12518479	0.99[ASN][1000 genomes]
rs12520628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12522647	0.87[ASN][1000 genomes]
rs12523278	0.83[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs13157657	0.81[ASN][1000 genomes]
rs13158675	0.99[ASN][1000 genomes]
rs13160801	0.81[ASN][1000 genomes]
rs13162358	0.99[ASN][1000 genomes]
rs13163970	0.81[ASN][1000 genomes]
rs13169711	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13170135	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13170262	0.81[ASN][1000 genomes]
rs13171757	0.89[ASN][1000 genomes]
rs13172080	0.81[ASN][1000 genomes]
rs13172084	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs13178686	0.99[ASN][1000 genomes]
rs13181015	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13186194	0.80[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs13188327	0.92[ASN][1000 genomes]
rs1348716	0.81[ASN][1000 genomes]
rs1374043	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1445976	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1445979	0.87[ASN][1000 genomes]
rs1477355	0.87[ASN][1000 genomes]
rs1986252	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053694	0.80[AMR][1000 genomes]
rs2276987	0.94[JPT][hapmap]
rs28610339	1.00[ASN][1000 genomes]
rs34739794	0.96[ASN][1000 genomes]
rs35262187	0.99[ASN][1000 genomes]
rs4276369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4391122	0.81[CEU][hapmap];0.88[YRI][hapmap]
rs4392578	0.99[ASN][1000 genomes]
rs4484384	0.99[ASN][1000 genomes]
rs4546329	0.83[MEX][hapmap]
rs4604142	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700418	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5027472	0.90[ASN][1000 genomes]
rs56035042	0.99[ASN][1000 genomes]
rs60529601	0.99[ASN][1000 genomes]
rs60886975	0.99[ASN][1000 genomes]
rs62368660	0.99[ASN][1000 genomes]
rs6449528	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449529	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449530	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6449531	1.00[ASN][1000 genomes]
rs6449532	1.00[ASN][1000 genomes]
rs6449533	1.00[ASN][1000 genomes]
rs6449535	0.87[ASN][1000 genomes]
rs6860608	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6873712	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6877610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6878927	0.80[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs6879809	0.88[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6881765	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6885005	1.00[ASN][1000 genomes]
rs6890351	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6894675	1.00[ASN][1000 genomes]
rs6895046	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6898746	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7700289	0.99[ASN][1000 genomes]
rs7701440	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7714457	0.81[ASN][1000 genomes]
rs7714712	1.00[ASN][1000 genomes]
rs7717082	0.81[ASN][1000 genomes]
rs7719647	0.81[ASN][1000 genomes]
rs7720894	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7722810	0.88[ASN][1000 genomes]
rs7724551	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727824	1.00[ASN][1000 genomes]
rs7732234	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7734879	1.00[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	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	esv2753894	chr5:60731458-60777345	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	22688191	GWAS catalog

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60711000-60735800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:60713400-60732800	Weak transcription	Small Intestine	intestine
3	chr5:60719800-60745200	Weak transcription	NHDF-Ad	bronchial
4	chr5:60720000-60733800	Weak transcription	NHLF	lung
5	chr5:60720000-60736400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:60720000-60737400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:60720400-60734000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:60720600-60743200	Weak transcription	HSMMtube	muscle
9	chr5:60721000-60733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:60725600-60732600	Weak transcription	Fetal Heart	heart
11	chr5:60725600-60737400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:60725800-60732800	Weak transcription	Esophagus	oesophagus
13	chr5:60725800-60732800	Weak transcription	Pancreas	Pancrea
14	chr5:60726000-60732800	Weak transcription	Left Ventricle	heart
15	chr5:60726000-60732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:60726000-60733800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:60726000-60736600	Weak transcription	Right Atrium	heart
18	chr5:60726800-60745600	Weak transcription	Stomach Mucosa	stomach
19	chr5:60727000-60732000	Weak transcription	Liver	Liver
20	chr5:60728400-60732400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:60728400-60732600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:60728400-60732600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:60728400-60733400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:60728400-60733600	Weak transcription	Fetal Brain Male	brain
25	chr5:60728400-60734000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:60728400-60734000	Weak transcription	HSMM	muscle
27	chr5:60728400-60737200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:60728400-60745400	Weak transcription	Ovary	ovary
29	chr5:60728600-60732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:60728600-60732800	Weak transcription	HMEC	breast
31	chr5:60728600-60732800	Weak transcription	NHEK	skin
32	chr5:60728600-60734000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:60728600-60734000	Weak transcription	Brain Germinal Matrix	brain
34	chr5:60728600-60737400	Weak transcription	Fetal Lung	lung
35	chr5:60728600-60737400	Weak transcription	Fetal Stomach	stomach
36	chr5:60728800-60732800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:60728800-60733800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:60728800-60737600	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:60729000-60732200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:60729000-60732600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:60729000-60737000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:60729600-60732200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:60729600-60733000	Weak transcription	Gastric	stomach
44	chr5:60730000-60731600	Enhancers	Brain Hippocampus Middle	brain
45	chr5:60730000-60732800	Weak transcription	Psoas Muscle	Psoas
46	chr5:60730200-60737600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr5:60730400-60733000	Enhancers	Brain Angular Gyrus	brain
48	chr5:60730400-60733200	Enhancers	Brain Cingulate Gyrus	brain
49	chr5:60730400-60735800	Enhancers	Brain Substantia Nigra	brain
50	chr5:60731000-60732000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links