Variant report

Variant	rs1085243
Chromosome Location	chr1:46544768-46544769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10789481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs10789485	0.82[CHD][hapmap]
rs10789486	0.82[CHD][hapmap]
rs10789487	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs10890361	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs10890363	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs10890370	0.82[CHD][hapmap]
rs10890378	0.82[CHD][hapmap]
rs10890380	0.82[CHD][hapmap]
rs10890381	0.82[CHD][hapmap]
rs10890383	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11211230	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs11211232	0.82[CHD][hapmap]
rs11211239	0.82[CHD][hapmap]
rs11211248	0.82[CHD][hapmap]
rs11579634	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs11589562	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap]
rs11810993	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs12021587	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs12049588	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap]
rs12132540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12133129	0.82[CHD][hapmap]
rs12139630	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs12144263	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap]
rs12409773	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap]
rs12561806	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs12564541	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs1613296	0.92[CHD][hapmap]
rs1707303	0.90[CHD][hapmap]
rs1707321	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1707322	0.92[CHD][hapmap]
rs1707333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1707336	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs1707340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs1768802	0.92[CHD][hapmap]
rs1768809	0.94[ASW][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs1768816	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2275426	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs2486445	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs4073846	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs4076006	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs4454479	0.82[CHD][hapmap]
rs4545281	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs4660321	0.80[JPT][hapmap];0.83[YRI][hapmap]
rs4660322	1.00[CEU][hapmap]
rs4660334	0.82[CHD][hapmap]
rs4660905	0.82[CHD][hapmap]
rs4660910	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6669522	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs6675726	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6675946	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs6677007	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs6686134	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs6698247	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs7522601	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs7526678	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs7538978	0.92[CHD][hapmap]
rs7556436	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs785464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785465	0.92[CHD][hapmap]
rs785468	0.92[CHD][hapmap]
rs785472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785479	0.83[YRI][hapmap]
rs785480	0.82[CHD][hapmap]
rs785481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs785484	0.90[CHD][hapmap]
rs785485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs785494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785495	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs785502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs785508	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs785509	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs785511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs785512	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs785520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs809774	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs809775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9429088	0.95[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9429183	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs946524	0.82[CHD][hapmap]
rs946527	0.82[CHD][hapmap]
rs946529	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1007750	chr1:46471293-46552564	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1085243	CMPK1	cis	cerebellum	SCAN
rs1085243	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs1085243	CYP4Z2P	cis	cerebellum	SCAN
rs1085243	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs1085243	MAST2	cis	cerebellum	SCAN
rs1085243	CYP4Z2P	cis	parietal	SCAN
rs1085243	IPP	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46501400-46548200	Weak transcription	Aorta	Aorta
2	chr1:46506000-46549400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:46508400-46546600	Weak transcription	HSMMtube	muscle
4	chr1:46510400-46548400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:46518200-46551600	Weak transcription	Psoas Muscle	Psoas
6	chr1:46524800-46547000	Weak transcription	Lung	lung
7	chr1:46525400-46548800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:46525600-46552600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:46527800-46546400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:46527800-46550400	Weak transcription	Fetal Heart	heart
11	chr1:46528600-46552200	Weak transcription	Thymus	Thymus
12	chr1:46528800-46550400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:46529000-46549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:46529400-46545200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:46529400-46545400	Weak transcription	Small Intestine	intestine
16	chr1:46531400-46546600	Weak transcription	HUVEC	blood vessel
17	chr1:46531800-46547200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:46532400-46575200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:46532800-46547200	Weak transcription	Right Ventricle	heart
20	chr1:46533400-46550200	Weak transcription	NH-A	brain
21	chr1:46535200-46547000	Weak transcription	Placenta	Placenta
22	chr1:46535200-46547000	Weak transcription	Fetal Stomach	stomach
23	chr1:46536400-46547400	Weak transcription	Fetal Lung	lung
24	chr1:46536600-46547000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:46536600-46547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:46537600-46547000	Weak transcription	Right Atrium	heart
27	chr1:46540400-46595200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:46541200-46595800	Weak transcription	Fetal Intestine Small	intestine
29	chr1:46541800-46550200	Weak transcription	Brain Germinal Matrix	brain
30	chr1:46542000-46549800	Weak transcription	Hela-S3	cervix
31	chr1:46542200-46547200	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:46542200-46548800	Weak transcription	GM12878-XiMat	blood
33	chr1:46542400-46550400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:46542800-46544800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:46543000-46549400	Weak transcription	Fetal Brain Female	brain
36	chr1:46543000-46564400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:46543400-46549400	Weak transcription	Dnd41	blood
38	chr1:46543600-46546200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:46543600-46547000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:46543600-46547000	Weak transcription	Left Ventricle	heart
41	chr1:46543800-46549800	Weak transcription	HSMM	muscle
42	chr1:46544000-46549800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:46544000-46549800	Weak transcription	HMEC	breast
44	chr1:46544400-46549400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:46544400-46549600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:46544600-46546400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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