Variant report

Variant	rs12584280
Chromosome Location	chr13:53621196-53621197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1112613	0.81[EUR][1000 genomes]
rs12429014	0.82[EUR][1000 genomes]
rs1343604	0.80[EUR][1000 genomes]
rs1891946	0.99[ASN][1000 genomes]
rs1936382	0.84[EUR][1000 genomes]
rs1936383	0.85[EUR][1000 genomes]
rs1936384	0.81[EUR][1000 genomes]
rs2185961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298234	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2806972	0.80[EUR][1000 genomes]
rs2806975	0.82[EUR][1000 genomes]
rs41292830	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886118	0.88[ASW][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap]
rs7333719	0.94[AMR][1000 genomes];0.98[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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12584280	PHF11	cis	cerebellum	SCAN
rs12584280	FNDC3A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53609000-53626400	Weak transcription	Small Intestine	intestine
2	chr13:53610800-53628800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:53616800-53621400	Enhancers	Fetal Stomach	stomach
4	chr13:53617400-53621800	Genic enhancers	Duodenum Mucosa	Duodenum
5	chr13:53618000-53624200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:53619200-53626600	Weak transcription	Gastric	stomach
7	chr13:53619400-53633000	Weak transcription	Pancreas	Pancrea
8	chr13:53619600-53626400	Weak transcription	Stomach Mucosa	stomach
9	chr13:53619800-53624200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:53620000-53623800	Weak transcription	Brain Germinal Matrix	brain
11	chr13:53620200-53621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:53620200-53624200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:53620200-53626600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr13:53620800-53621200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:53620800-53621200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:53620800-53622800	Weak transcription	Fetal Kidney	kidney
17	chr13:53621000-53621600	Enhancers	Fetal Muscle Leg	muscle

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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