Variant report

Variant	rs2291989
Chromosome Location	chr3:134872540-134872541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134870327..134872584-chr3:134875480..134877102,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10804635	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1159404	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11712935	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492126	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs12636613	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12636659	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13063564	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs13076510	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13087756	0.98[ASN][1000 genomes]
rs1392918	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1404577	0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1501205	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1501206	0.93[ASN][1000 genomes]
rs1501207	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1880531	0.81[CHD][hapmap]
rs2270882	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3772638	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3772640	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3772647	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3772648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3821503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7372088	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7373413	0.82[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7620133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7642038	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs940639	0.83[CHD][hapmap]
rs9845406	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9883173	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[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	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv829731	chr3:134711713-134885064	Strong transcription Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2291989	PRR23C	cis	parietal	SCAN
rs2291989	PPP2R3A	cis	parietal	SCAN
rs2291989	TXNDC6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134823000-134880000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:134859600-134873600	Weak transcription	Right Ventricle	heart
3	chr3:134861000-134878200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:134861600-134880600	Weak transcription	Fetal Brain Female	brain
5	chr3:134867800-134884800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:134868000-134876800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:134868000-134878400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:134868000-134878400	Weak transcription	Fetal Brain Male	brain
9	chr3:134868600-134878600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:134868600-134883800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:134869000-134878600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:134869200-134873200	Weak transcription	Psoas Muscle	Psoas
13	chr3:134869800-134872800	Weak transcription	Liver	Liver
14	chr3:134870200-134872600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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