Variant report

Variant	rs315542
Chromosome Location	chr1:84839197-84839198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493748	0.81[EUR][1000 genomes]
rs11805246	0.84[EUR][1000 genomes]
rs1690702	0.81[CHB][hapmap]
rs17131613	0.89[GIH][hapmap]
rs172735	0.81[CHB][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs178367	0.81[CHB][hapmap];0.88[MEX][hapmap]
rs186405	0.81[CHB][hapmap];0.82[AMR][1000 genomes]
rs315525	0.81[CHB][hapmap]
rs315526	0.81[CHB][hapmap]
rs315527	0.81[CHB][hapmap]
rs315528	0.89[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs315530	0.81[CHB][hapmap]
rs315531	0.81[CHB][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs315535	0.85[AMR][1000 genomes]
rs315541	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315543	0.94[ASN][1000 genomes]
rs315544	0.94[ASN][1000 genomes]
rs315547	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs315552	0.81[CHB][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs315553	0.81[CHB][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs315554	0.81[CHB][hapmap]
rs315555	0.81[CHB][hapmap]
rs316660	0.81[CHB][hapmap]
rs316661	0.81[CHB][hapmap]
rs316662	0.81[CHB][hapmap]
rs316663	0.81[CHB][hapmap]
rs316664	0.81[CHB][hapmap]
rs487220	0.94[ASN][1000 genomes]
rs575277	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs642774	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670075	0.84[EUR][1000 genomes]
rs7521357	0.84[EUR][1000 genomes]
rs786653	0.94[AMR][1000 genomes];0.81[EUR][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	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs315542	HIVEP2	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84829800-84840400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:84832600-84842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:84833200-84842800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:84833600-84839200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:84834800-84839200	Weak transcription	Fetal Heart	heart
6	chr1:84836200-84840800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:84836600-84841800	Weak transcription	Fetal Brain Male	brain
8	chr1:84836800-84839400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:84836800-84839600	Weak transcription	Osteobl	bone
10	chr1:84837000-84839800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:84837000-84840200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:84837000-84841800	Weak transcription	NHLF	lung
13	chr1:84837000-84842000	Weak transcription	NH-A	brain
14	chr1:84837200-84840400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:84837200-84842600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:84837400-84840400	Weak transcription	NHDF-Ad	bronchial
17	chr1:84837400-84840600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:84837400-84840600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:84837600-84840400	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:84837800-84841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:84838000-84840800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:84838400-84843800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:84838600-84843200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:84838600-84843600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:84838800-84839600	Weak transcription	Psoas Muscle	Psoas
26	chr1:84838800-84840200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:84839000-84839400	Enhancers	HSMMtube	muscle
28	chr1:84839000-84839800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links