Variant report

Variant	rs9296477
Chromosome Location	chr6:46027383-46027384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10484840	0.87[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13328271	1.00[JPT][hapmap]
rs1578005	1.00[JPT][hapmap]
rs2179993	1.00[JPT][hapmap]
rs3777597	1.00[JPT][hapmap]
rs6906803	1.00[JPT][hapmap]
rs6919720	1.00[JPT][hapmap]
rs6922977	1.00[JPT][hapmap]
rs6927513	0.87[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6936849	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs73464404	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9463167	1.00[JPT][hapmap]
rs9472662	1.00[JPT][hapmap]
rs9472666	1.00[JPT][hapmap]
rs9472667	1.00[JPT][hapmap]
rs9472670	1.00[JPT][hapmap]
rs9472674	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428482	chr6:45926644-46050182	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1025846	chr6:45955173-46047269	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9296477	KRTAP12-4	trans	cerebellum	SCAN
rs9296477	NFKBIE	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46022800-46028400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:46023800-46028600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:46026400-46027400	Enhancers	Fetal Intestine Small	intestine
4	chr6:46026400-46027600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:46026400-46029200	Weak transcription	Liver	Liver
6	chr6:46026600-46027400	Enhancers	Psoas Muscle	Psoas
7	chr6:46026800-46027400	Weak transcription	Pancreas	Pancrea
8	chr6:46026800-46027600	Enhancers	Adipose Nuclei	Adipose
9	chr6:46026800-46027600	Enhancers	Right Atrium	heart
10	chr6:46026800-46031400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:46027000-46028000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:46027000-46030000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:46027000-46032200	Enhancers	Fetal Intestine Large	intestine
14	chr6:46027200-46027400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:46027200-46027600	Enhancers	Right Ventricle	heart
16	chr6:46027200-46027800	Enhancers	Fetal Heart	heart
17	chr6:46027200-46028400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:46027200-46030800	Enhancers	Sigmoid Colon	Sigmoid Colon

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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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