Variant report

Variant	rs1992214
Chromosome Location	chr8:105744498-105744499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1000420	0.83[CHB][hapmap]
rs1000421	0.83[CHB][hapmap]
rs10102865	0.83[CHB][hapmap]
rs10103495	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10505064	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955358	0.83[ASN][1000 genomes]
rs11783360	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12542435	0.81[CHB][hapmap]
rs13250808	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13261792	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13271748	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1370797	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1438343	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1442497	0.85[ASN][1000 genomes]
rs1992211	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118603	0.83[CHB][hapmap]
rs28548678	0.86[ASN][1000 genomes]
rs3847142	0.86[ASN][1000 genomes]
rs3847143	0.83[CHB][hapmap]
rs3847144	0.86[ASN][1000 genomes]
rs3910535	0.81[ASN][1000 genomes]
rs4294157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734809	0.85[ASN][1000 genomes]
rs4734810	0.83[CHB][hapmap]
rs4734811	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs4734812	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4734817	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6983576	0.86[ASN][1000 genomes]
rs6984657	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6994484	0.85[ASN][1000 genomes]
rs7014956	0.85[ASN][1000 genomes]
rs725403	0.85[ASN][1000 genomes]
rs7826497	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7845583	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv2422460	chr8:105573376-105746329	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1032476	chr8:105609904-106030916	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv539710	chr8:105609904-106030916	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1992214	ABRA	cis	cerebellum	SCAN
rs1992214	TPM2	trans	lymphoblastoid	seeQTL
rs1992214	LRP12	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105743200-105744600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:105743200-105745200	Enhancers	NHEK	skin
3	chr8:105743400-105744600	Enhancers	Fetal Thymus	thymus
4	chr8:105743400-105744800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:105743400-105744800	Enhancers	Brain Germinal Matrix	brain
6	chr8:105743400-105744800	Enhancers	NH-A	brain
7	chr8:105743600-105744600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr8:105743600-105744600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:105743800-105744600	Active TSS	Brain Hippocampus Middle	brain
10	chr8:105744000-105744600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr8:105744000-105744600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr8:105744000-105744600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr8:105744000-105744800	Active TSS	Brain Anterior Caudate	brain
14	chr8:105744000-105744800	Flanking Active TSS	Fetal Brain Male	brain
15	chr8:105744000-105744800	Flanking Active TSS	Fetal Brain Female	brain
16	chr8:105744000-105746000	Enhancers	Primary T cells from cord blood	blood
17	chr8:105744200-105744600	Active TSS	Brain Angular Gyrus	brain
18	chr8:105744200-105744600	Active TSS	Ovary	ovary
19	chr8:105744200-105744600	Bivalent Enhancer	K562	blood
20	chr8:105744200-105744800	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr8:105744400-105744600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:105744400-105744600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:105744400-105744800	Flanking Active TSS	Brain Cingulate Gyrus	brain

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