Variant report

Variant	rs2399688
Chromosome Location	chr11:93304483-93304484
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	chr11:93298565..93302751-chr11:93303785..93308130,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10831063	0.86[ASN][1000 genomes]
rs10831064	0.86[ASN][1000 genomes]
rs11020417	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11020420	0.88[EUR][1000 genomes]
rs11020421	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11020426	0.84[ASN][1000 genomes]
rs11020427	0.86[ASN][1000 genomes]
rs12222957	0.80[ASN][1000 genomes]
rs1954783	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2399686	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34679231	0.85[ASN][1000 genomes]
rs4237559	0.87[ASN][1000 genomes]
rs4753089	0.87[ASN][1000 genomes]
rs4753093	0.81[ASN][1000 genomes]
rs4753472	0.82[AMR][1000 genomes]
rs4753480	0.90[ASN][1000 genomes]
rs7120590	0.87[ASN][1000 genomes]

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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2399688	C11orf54	cis	parietal	SCAN
rs2399688	SCARNA9	cis	cerebellum	SCAN
rs2399688	PIWIL4	cis	parietal	SCAN
rs2399688	MED17	cis	parietal	SCAN
rs2399688	FN5	cis	multi-tissue	Pritchard
rs2399688	SCARNA9	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93300200-93305200	Enhancers	Liver	Liver
2	chr11:93300800-93305000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:93301000-93304600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:93301000-93306400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:93302200-93310400	Weak transcription	Psoas Muscle	Psoas
6	chr11:93302800-93305200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:93302800-93305800	Enhancers	A549	lung
8	chr11:93303000-93304600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr11:93303000-93304800	Enhancers	Fetal Intestine Large	intestine
10	chr11:93303000-93305800	Enhancers	HepG2	liver
11	chr11:93303400-93304800	Enhancers	Adipose Nuclei	Adipose
12	chr11:93303400-93305200	Enhancers	Duodenum Mucosa	Duodenum
13	chr11:93303600-93304600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:93303600-93304800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:93303600-93305200	Enhancers	Fetal Intestine Small	intestine
16	chr11:93303800-93304600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:93303800-93304600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr11:93303800-93304600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:93303800-93304600	Flanking Active TSS	Hela-S3	cervix
20	chr11:93303800-93304600	Enhancers	Osteobl	bone
21	chr11:93304000-93304800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:93304000-93305200	Enhancers	Pancreas	Pancrea
23	chr11:93304000-93305400	Enhancers	Placenta	Placenta
24	chr11:93304200-93304600	Enhancers	Fetal Kidney	kidney
25	chr11:93304200-93304600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr11:93304200-93304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:93304200-93305600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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