Variant report

Variant	rs9532399
Chromosome Location	chr13:40138671-40138672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1885759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324337	0.91[EUR][1000 genomes]
rs35396912	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35801450	0.81[AMR][1000 genomes]
rs7322336	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333056	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7981547	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7982917	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9315701	0.91[EUR][1000 genomes]
rs9315702	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9315703	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9315706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315707	0.88[EUR][1000 genomes]
rs9532396	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9548804	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548805	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548817	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548819	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548820	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548821	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548822	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548824	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548826	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548829	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548831	0.82[AMR][1000 genomes]
rs9603564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:40130000-40139600	Weak transcription	Fetal Stomach	stomach
5	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:40134000-40139400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:40134200-40139800	Weak transcription	Fetal Muscle Leg	muscle
8	chr13:40135400-40139600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:40135400-40139800	Weak transcription	Right Atrium	heart
10	chr13:40135800-40139200	Enhancers	NHEK	skin
11	chr13:40135800-40139400	Enhancers	HMEC	breast
12	chr13:40135800-40142000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:40135800-40145600	Weak transcription	Lung	lung
14	chr13:40136200-40138800	Enhancers	NHDF-Ad	bronchial
15	chr13:40136200-40139000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:40136200-40139600	Enhancers	HSMM	muscle
17	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
18	chr13:40136800-40138800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:40136800-40138800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr13:40136800-40139000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:40136800-40139000	Enhancers	Osteobl	bone
22	chr13:40136800-40140800	Enhancers	Ovary	ovary
23	chr13:40136800-40141200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:40137000-40138800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:40137000-40139200	Enhancers	NH-A	brain
26	chr13:40137000-40139400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:40137000-40139600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:40137000-40139600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:40137000-40139600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr13:40137000-40140600	Enhancers	Fetal Heart	heart
31	chr13:40137200-40139400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:40137400-40138800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:40137400-40139200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr13:40137400-40139200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:40137600-40139200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr13:40137600-40139600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr13:40137600-40139600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr13:40137600-40139600	Enhancers	Brain Hippocampus Middle	brain
39	chr13:40137600-40140200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr13:40137600-40140200	Enhancers	Colon Smooth Muscle	Colon
41	chr13:40137800-40138800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:40137800-40139000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr13:40138000-40138800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:40138000-40138800	Enhancers	Aorta	Aorta
45	chr13:40138200-40138800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr13:40138200-40139000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr13:40138200-40139000	Weak transcription	Fetal Lung	lung
48	chr13:40138200-40139200	Weak transcription	Fetal Brain Female	brain
49	chr13:40138200-40139600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr13:40138200-40139600	Weak transcription	Rectal Smooth Muscle	rectum

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