Variant report

Variant	rs280726
Chromosome Location	chr2:35069359-35069360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10191460	0.94[ASN][1000 genomes]
rs11680038	0.94[ASN][1000 genomes]
rs13417686	0.96[ASN][1000 genomes]
rs280691	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs280692	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs280696	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs280697	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs280698	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs280702	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs280709	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280710	0.84[EUR][1000 genomes]
rs280711	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280713	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs280715	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs280722	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28767616	0.96[ASN][1000 genomes]
rs371118	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs383473	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs391835	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6744589	0.96[ASN][1000 genomes]
rs7600597	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873821	chr2:34738616-35416075	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1003361	chr2:34746445-35202302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873825	chr2:34892832-35115848	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1003322	chr2:34898412-35216795	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv524038	chr2:34990937-35073607	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv873831	chr2:35013851-35092762	ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv873832	chr2:35013851-35095373	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873833	chr2:35022419-35115848	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1837864	chr2:35030699-35115979	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873834	chr2:35037733-35138518	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv428030	chr2:35051843-35286924	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv516465	chr2:35061211-35073607	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv522582	chr2:35065246-35088235	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs280726	PLCH2	trans	parietal	SCAN
rs280726	PRKD3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:35057200-35080400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:35069200-35069400	Enhancers	HUES6 Cell Line	embryonic stem cell

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