Variant report

Variant	rs552125
Chromosome Location	chr13:110938813-110938814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11617955	1.00[CHB][hapmap]
rs12866570	1.00[CHB][hapmap]
rs13260	1.00[CHB][hapmap]
rs551212	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes]
rs56258703	1.00[ASN][1000 genomes]
rs58455864	1.00[ASN][1000 genomes]
rs594377	1.00[CHB][hapmap]
rs595325	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs61963337	1.00[ASN][1000 genomes]
rs61963356	1.00[ASN][1000 genomes]
rs61963357	1.00[ASN][1000 genomes]
rs61963358	1.00[ASN][1000 genomes]
rs61964261	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621929	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs622253	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs623157	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs668149	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7336547	1.00[CHD][hapmap]
rs73617438	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984789	1.00[CHD][hapmap]
rs9521727	1.00[CHD][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	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
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs552125	C13orf16	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110917400-110939000	Weak transcription	Fetal Intestine Large	intestine
2	chr13:110920200-110951200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:110925400-110949000	Weak transcription	Fetal Kidney	kidney
4	chr13:110927400-110939000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:110928600-110951000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:110931400-110941400	Weak transcription	Fetal Intestine Small	intestine
7	chr13:110932600-110939200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:110933000-110939200	Enhancers	Colon Smooth Muscle	Colon
9	chr13:110934000-110940000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:110934000-110940400	Enhancers	Fetal Heart	heart
11	chr13:110934000-110941400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:110934400-110945400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:110934600-110940400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr13:110935000-110939400	Enhancers	Rectal Smooth Muscle	rectum
15	chr13:110935600-110940400	Enhancers	Right Atrium	heart
16	chr13:110935800-110939000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr13:110935800-110940200	Enhancers	Lung	lung
18	chr13:110935800-110940200	Genic enhancers	NH-A	brain
19	chr13:110935800-110940400	Genic enhancers	Adipose Nuclei	Adipose
20	chr13:110936000-110940200	Enhancers	NHDF-Ad	bronchial
21	chr13:110936200-110940600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr13:110936200-110951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr13:110936200-110958800	Weak transcription	Gastric	stomach
24	chr13:110936400-110939200	Weak transcription	Stomach Mucosa	stomach
25	chr13:110936600-110939000	Weak transcription	Psoas Muscle	Psoas
26	chr13:110936600-110939000	Weak transcription	HSMMtube	muscle
27	chr13:110936600-110939400	Weak transcription	Fetal Lung	lung
28	chr13:110936600-110941400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:110937000-110943200	Weak transcription	Colonic Mucosa	Colon
30	chr13:110937000-110955400	Weak transcription	A549	lung
31	chr13:110937200-110939200	Genic enhancers	Left Ventricle	heart
32	chr13:110937200-110939600	Enhancers	Aorta	Aorta
33	chr13:110937200-110940200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:110937200-110940400	Enhancers	Placenta	Placenta
35	chr13:110937400-110939400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr13:110937400-110941400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:110937400-110951000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:110937400-110952000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:110937600-110940000	Genic enhancers	Fetal Stomach	stomach
40	chr13:110937600-110940200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr13:110937800-110939200	Strong transcription	HSMM	muscle
42	chr13:110937800-110946000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:110937800-110947600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:110937800-110950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr13:110938000-110939600	Enhancers	Pancreas	Pancrea
46	chr13:110938000-110951200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:110938200-110939000	Weak transcription	HUVEC	blood vessel
48	chr13:110938200-110939200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:110938200-110940200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:110938200-110940400	Enhancers	Ovary	ovary

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