Variant report

Variant	rs828053
Chromosome Location	chr1:97609326-97609327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10783055	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875050	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875051	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875052	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165791	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165792	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11165795	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165798	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs11165800	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165803	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11165804	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165805	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12029380	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12035468	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12041436	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12091136	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120077	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122422	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12124552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12134860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12740796	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12759852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1514495	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs1514497	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs17116479	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs1760209	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1760210	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17702702	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2039449	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2991263	0.86[ASN][1000 genomes]
rs34031151	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4309030	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4390222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593633	0.87[ASN][1000 genomes]
rs6593634	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6668653	0.85[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670102	0.81[JPT][hapmap]
rs7520102	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8179310	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs828057	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828059	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs864341	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs993714	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830692	chr1:97501492-97625153	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs828053	VCAM1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97563600-97619200	Weak transcription	Dnd41	blood
2	chr1:97564200-97632800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:97585600-97621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:97597400-97619600	Weak transcription	Liver	Liver
5	chr1:97603400-97610200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:97604000-97610000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:97604000-97620000	Weak transcription	Pancreas	Pancrea
8	chr1:97604200-97610400	Weak transcription	Fetal Brain Male	brain
9	chr1:97604400-97609600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:97604400-97611000	Weak transcription	Stomach Mucosa	stomach
11	chr1:97604400-97614800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:97604400-97629000	Weak transcription	Primary B cells from cord blood	blood
13	chr1:97604600-97609400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:97604600-97609400	Weak transcription	A549	lung
15	chr1:97604600-97609400	Weak transcription	HUVEC	blood vessel
16	chr1:97604600-97609600	Weak transcription	HSMMtube	muscle
17	chr1:97604600-97609800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:97604600-97609800	Weak transcription	Brain Angular Gyrus	brain
19	chr1:97604600-97610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:97604600-97614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:97606200-97610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:97606200-97626600	Weak transcription	Ovary	ovary
23	chr1:97606800-97610400	Weak transcription	Primary T cells from cord blood	blood
24	chr1:97606800-97610400	Weak transcription	Aorta	Aorta
25	chr1:97607200-97611000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:97607400-97612600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:97608000-97609600	Enhancers	NH-A	brain
28	chr1:97608000-97610200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:97608200-97609400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:97608600-97610200	Enhancers	Brain Substantia Nigra	brain
31	chr1:97608800-97610400	Enhancers	Osteobl	bone
32	chr1:97608800-97611200	Enhancers	NHEK	skin
33	chr1:97608800-97611400	Enhancers	Hela-S3	cervix
34	chr1:97608800-97611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:97608800-97612000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:97608800-97612000	Enhancers	HMEC	breast
37	chr1:97608800-97612200	Enhancers	Brain Anterior Caudate	brain
38	chr1:97608800-97612200	Enhancers	NHDF-Ad	bronchial
39	chr1:97608800-97612400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:97609000-97609400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:97609000-97609600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:97609000-97610400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:97609000-97610400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:97609000-97610600	Enhancers	Brain Hippocampus Middle	brain
45	chr1:97609000-97611000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:97609000-97611200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:97609000-97611600	Enhancers	HSMM	muscle
48	chr1:97609000-97612000	Enhancers	NHLF	lung
49	chr1:97609200-97611600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:97609200-97612000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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