Variant report

Variant	rs2651316
Chromosome Location	chr3:147059334-147059335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10513309	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10935665	0.83[EUR][1000 genomes]
rs1394046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1500867	0.86[EUR][1000 genomes]
rs1503733	0.81[YRI][hapmap]
rs17567518	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2133939	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2651315	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2654819	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2654820	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681356	0.85[CHD][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes]
rs62275345	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7629647	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7639019	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs884370	0.91[ASW][hapmap];1.00[CEU][hapmap];0.97[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385588	chr3:146782324-147083081	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1013080	chr3:147008962-147167690	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536763	chr3:147008962-147167690	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2651316	P2RY14	cis	cerebellum	SCAN
rs2651316	MBNL1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:147057400-147059600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:147057600-147060200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr3:147057600-147060600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:147057600-147060600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:147057600-147060600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:147057800-147060000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:147057800-147060400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:147057800-147060800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:147058400-147059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:147058600-147060600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:147058800-147059400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:147058800-147060000	Enhancers	H1 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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