Variant report

Variant	rs1534232
Chromosome Location	chr12:56035129-56035130
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10783765	0.80[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10783766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876842	0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10876843	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526419	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534230	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1534231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3953272	0.83[ASN][1000 genomes]
rs4759176	0.84[LWK][hapmap];0.88[YRI][hapmap]
rs7133243	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7139287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv559001	chr12:55507465-56057708	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3490751	chr12:56030785-56035633	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3490754	chr12:56031235-56035533	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3490750	chr12:56031555-56035542	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1534232	R3HDM2	cis	parietal	SCAN
rs1534232	RAB5B	cis	parietal	SCAN
rs1534232	KIAA0748	cis	parietal	SCAN
rs1534232	SARNP	cis	parietal	SCAN
rs1534232	DCD	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56023200-56036800	Weak transcription	Spleen	Spleen
2	chr12:56025800-56035200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:56030800-56035800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:56031000-56035200	Weak transcription	Left Ventricle	heart
5	chr12:56032200-56036200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:56032600-56036000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:56032800-56040000	Weak transcription	Right Atrium	heart
8	chr12:56033800-56041400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:56034000-56035200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:56034800-56035600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:56034800-56035800	Enhancers	Primary B cells from cord blood	blood
12	chr12:56034800-56037400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:56035000-56037400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr12:56035000-56037600	Enhancers	Primary B cells from peripheral blood	blood

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

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