Variant report

Variant	rs2890342
Chromosome Location	chr1:247436234-247436235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10754543	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs10802482	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10802483	0.89[EUR][1000 genomes]
rs11579326	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11581163	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12081945	0.84[EUR][1000 genomes]
rs12082983	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12564303	0.82[EUR][1000 genomes]
rs12566166	0.89[EUR][1000 genomes]
rs1771918	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17721193	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1778552	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1778553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2211273	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268345	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4925606	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55686936	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913685	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56124448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56245379	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56250713	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56358050	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57647632	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58747962	0.81[ASN][1000 genomes]
rs61838684	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61838689	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61841570	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6426236	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656258	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667658	0.88[EUR][1000 genomes]
rs6698384	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698803	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544023	0.88[EUR][1000 genomes]
rs7552041	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv549587	chr1:247400259-247438446	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2890342	VN1R5	cis	cerebellum	SCAN
rs2890342	EXO1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247433600-247436400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:247433600-247436600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:247436000-247436400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:247436000-247436400	Enhancers	HSMMtube	muscle
5	chr1:247436000-247436800	Enhancers	Fetal Kidney	kidney
6	chr1:247436000-247436800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:247436000-247436800	Enhancers	Placenta	Placenta
8	chr1:247436200-247436800	Enhancers	Psoas Muscle	Psoas
9	chr1:247436200-247436800	Enhancers	HSMM	muscle
10	chr1:247436200-247437000	Enhancers	Cortex derived primary cultured neurospheres	brain

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