Variant report

Variant	rs3005896
Chromosome Location	chr1:56785831-56785832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2994548	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994549	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994550	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994551	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994552	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994554	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2994555	0.80[AMR][1000 genomes]
rs2994556	0.80[AMR][1000 genomes]
rs3005888	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3005889	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3005890	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3005892	0.80[AMR][1000 genomes]
rs3005893	0.80[AMR][1000 genomes]
rs3005894	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3005895	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3005897	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005898	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005899	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3005900	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3005902	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3005904	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3005905	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3005909	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9787000	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1015037	chr1:56784322-56814739	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3005896	PPAP2B	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56757800-56786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:56765200-56795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:56768200-56791000	Weak transcription	Aorta	Aorta
4	chr1:56769600-56788000	Weak transcription	Right Atrium	heart
5	chr1:56770000-56791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:56770400-56792200	Weak transcription	Right Ventricle	heart
7	chr1:56770600-56786600	Weak transcription	Left Ventricle	heart
8	chr1:56780200-56786200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:56780200-56786600	Weak transcription	Psoas Muscle	Psoas
10	chr1:56780400-56793600	Weak transcription	Liver	Liver
11	chr1:56781800-56791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:56782000-56797000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:56782600-56786200	Weak transcription	Fetal Stomach	stomach
14	chr1:56784200-56788000	Enhancers	NHDF-Ad	bronchial
15	chr1:56784200-56791000	Weak transcription	Ovary	ovary
16	chr1:56784200-56792200	Weak transcription	Lung	lung
17	chr1:56785000-56786200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:56785600-56787000	Enhancers	Fetal Lung	lung
19	chr1:56785600-56787200	Enhancers	Fetal Muscle Leg	muscle
20	chr1:56785600-56787400	Enhancers	Fetal Heart	heart
21	chr1:56785800-56787000	Enhancers	Stomach Smooth Muscle	stomach

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