Variant report

Variant	rs56225239
Chromosome Location	chr3:112577779-112577780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10934203	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10934204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10934205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11914890	0.92[EUR][1000 genomes]
rs16860078	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16860199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55858804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56139709	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56160012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56170322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56232399	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72948499	0.88[EUR][1000 genomes]
rs72950311	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3501334	chr3:112546820-112648766	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3501335	chr3:112546820-112648766	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112574400-112578200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:112574600-112578600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:112574800-112578400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:112575000-112577800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:112575000-112578000	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:112575200-112577800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:112575200-112578200	Enhancers	Primary B cells from cord blood	blood
8	chr3:112575200-112578800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:112575800-112578000	ZNF genes & repeats	GM12878-XiMat	blood
10	chr3:112576400-112578000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:112576400-112578400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:112576800-112577800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr3:112576800-112578000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:112577000-112577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:112577400-112577800	Enhancers	A549	lung
16	chr3:112577400-112577800	Enhancers	K562	blood
17	chr3:112577400-112578000	Enhancers	NH-A	brain

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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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