Variant report

Variant	rs9521666
Chromosome Location	chr13:110897444-110897445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12873154	1.00[ASW][hapmap]
rs613430	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614282	0.91[ASN][1000 genomes]
rs614786	0.91[ASN][1000 genomes]
rs678661	0.91[ASN][1000 genomes]
rs679062	0.91[ASN][1000 genomes]
rs679097	0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs693831	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139637	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7337819	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338566	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs7338606	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751749	0.91[CEU][hapmap];0.86[TSI][hapmap]
rs9515173	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9521660	0.87[ASN][1000 genomes]
rs9521665	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9521673	0.86[CEU][hapmap]
rs9559749	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9634591	1.00[ASW][hapmap]

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	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv521901	chr13:110895995-110897444	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9521666	C13orf16	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110869000-110898800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr13:110881400-110899800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:110881600-110900600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr13:110882400-110900400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:110882600-110898800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:110882600-110899600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr13:110882600-110913600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr13:110882800-110900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:110884200-110902200	Weak transcription	HMEC	breast
10	chr13:110884600-110902400	Weak transcription	NHEK	skin
11	chr13:110884800-110914000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:110885200-110899000	Weak transcription	Fetal Intestine Large	intestine
13	chr13:110889600-110900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:110889600-110900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:110889600-110904200	Enhancers	NHDF-Ad	bronchial
16	chr13:110890200-110899400	Enhancers	Left Ventricle	heart
17	chr13:110890800-110901800	Enhancers	Fetal Heart	heart
18	chr13:110891400-110908600	Weak transcription	Psoas Muscle	Psoas
19	chr13:110892200-110898400	Weak transcription	Fetal Lung	lung
20	chr13:110892200-110899000	Weak transcription	Fetal Kidney	kidney
21	chr13:110892600-110897800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr13:110893000-110898600	Weak transcription	Gastric	stomach
23	chr13:110893200-110899000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:110893400-110897800	Strong transcription	HUVEC	blood vessel
25	chr13:110894000-110899000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:110894400-110900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr13:110894600-110912200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:110895200-110898000	Weak transcription	HSMMtube	muscle
29	chr13:110895200-110903800	Enhancers	Colon Smooth Muscle	Colon
30	chr13:110895400-110897800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr13:110895400-110899000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr13:110895400-110899000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr13:110895400-110899200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr13:110895600-110898000	Weak transcription	Placenta	Placenta
35	chr13:110895600-110898800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:110895600-110898800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr13:110895600-110903800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:110896000-110897600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr13:110896000-110897800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr13:110896000-110898400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:110896000-110899800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:110896000-110900600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:110896000-110904400	Enhancers	NHLF	lung
44	chr13:110896200-110904400	Enhancers	Rectal Smooth Muscle	rectum
45	chr13:110896400-110897800	Weak transcription	HSMM	muscle
46	chr13:110896600-110898200	Genic enhancers	Fetal Stomach	stomach
47	chr13:110896800-110897600	Enhancers	Small Intestine	intestine
48	chr13:110896800-110897800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:110896800-110898000	Enhancers	Duodenum Mucosa	Duodenum
50	chr13:110896800-110898200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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