Variant report

Variant	rs2612025
Chromosome Location	chr3:53778314-53778315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53777857..53780018-chr3:53784994..53786883,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1020820	0.85[CEU][hapmap]
rs1020821	0.85[CEU][hapmap]
rs1809282	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2015263	0.92[EUR][1000 genomes]
rs2016271	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2169143	0.85[CEU][hapmap]
rs2169144	0.85[CEU][hapmap]
rs2577325	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2577327	0.94[EUR][1000 genomes]
rs2577328	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2577329	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2577331	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2612023	0.93[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2612024	0.93[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2612026	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2612027	0.83[MKK][hapmap]
rs2612029	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2612030	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs2612033	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2612034	0.85[CEU][hapmap]
rs2633725	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2633727	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2680649	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2680651	0.87[EUR][1000 genomes]
rs2680652	0.82[CEU][hapmap]
rs2680664	0.85[CEU][hapmap]
rs2680669	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2680670	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774554	0.83[CEU][hapmap]
rs7373113	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7373253	0.93[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs755886	0.93[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7649275	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs877257	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs898419	0.92[CEU][hapmap];0.84[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2612025	RAD54L2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
2	chr3:53764200-53779800	Weak transcription	Liver	Liver
3	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
7	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:53766600-53781200	Weak transcription	Lung	lung
10	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
11	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
15	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53775800-53779400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:53777600-53778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:53777800-53778600	Enhancers	Gastric	stomach
21	chr3:53777800-53778800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:53777800-53779000	Enhancers	Fetal Thymus	thymus
23	chr3:53777800-53787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:53778000-53778800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:53778000-53778800	Enhancers	Pancreas	Pancrea
26	chr3:53778000-53778800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:53778000-53779800	Enhancers	GM12878-XiMat	blood
28	chr3:53778200-53778400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:53778200-53778600	Enhancers	Fetal Muscle Leg	muscle

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