Variant report

Variant	rs16856887
Chromosome Location	chr2:11064628-11064629
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1467993	0.80[GIH][hapmap]
rs34555948	0.87[EUR][1000 genomes]
rs35427546	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35964524	0.85[EUR][1000 genomes]
rs921605	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580969	chr2:11033567-11081645	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv521177	chr2:11040146-11066699	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv833392	chr2:11054580-11235239	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv817618	chr2:11055298-11075754	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv469438	chr2:11055298-11085744	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv580970	chr2:11055298-11085744	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	nsv523537	chr2:11061156-11075317	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16856887	MAP4K5	trans	cerebellum	SCAN
rs16856887	MBOAT2	cis	cerebellum	SCAN
rs16856887	ROCK2	cis	parietal	SCAN
rs16856887	IAH1	cis	cerebellum	SCAN
rs16856887	ASAP2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11054400-11072400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:11055200-11069800	Weak transcription	A549	lung
3	chr2:11057000-11069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:11057600-11070600	Weak transcription	Fetal Brain Female	brain
5	chr2:11059800-11067600	Weak transcription	Right Atrium	heart
6	chr2:11060600-11066400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:11061800-11069800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:11063000-11066400	Weak transcription	Fetal Brain Male	brain
9	chr2:11063200-11064800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:11063400-11064800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:11063600-11064800	Weak transcription	Fetal Thymus	thymus
12	chr2:11064200-11065200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:11064400-11065000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:11064600-11064800	Enhancers	NHLF	lung
15	chr2:11064600-11065200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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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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