Variant report

Variant	rs61956464
Chromosome Location	chr13:40139570-40139571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12853787	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1548273	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17060288	0.84[ASN][1000 genomes]
rs2324348	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34490304	1.00[EUR][1000 genomes]
rs4551908	0.80[ASN][1000 genomes]
rs56103901	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213801	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57628663	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61432896	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61954148	0.96[ASN][1000 genomes]
rs61956463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61956467	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423201	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7317222	0.94[ASN][1000 genomes]
rs7333551	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7334762	0.96[ASN][1000 genomes]
rs74044105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74046534	0.96[ASN][1000 genomes]
rs74046537	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs74046538	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs74046541	0.96[ASN][1000 genomes]
rs74046546	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs74046552	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs74046553	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs74046554	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs74046555	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs74046556	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7983392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532392	0.94[ASN][1000 genomes]
rs978136	0.96[EUR][1000 genomes];0.96[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:65 , 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	chr13:40134200-40139800	Weak transcription	Fetal Muscle Leg	muscle
7	chr13:40135400-40139600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:40135400-40139800	Weak transcription	Right Atrium	heart
9	chr13:40135800-40142000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:40135800-40145600	Weak transcription	Lung	lung
11	chr13:40136200-40139600	Enhancers	HSMM	muscle
12	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
13	chr13:40136800-40140800	Enhancers	Ovary	ovary
14	chr13:40136800-40141200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr13:40137000-40139600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:40137000-40139600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:40137000-40139600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr13:40137000-40140600	Enhancers	Fetal Heart	heart
19	chr13:40137600-40139600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr13:40137600-40139600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr13:40137600-40139600	Enhancers	Brain Hippocampus Middle	brain
22	chr13:40137600-40140200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr13:40137600-40140200	Enhancers	Colon Smooth Muscle	Colon
24	chr13:40138200-40139600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:40138200-40139600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:40138400-40139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr13:40138400-40139800	Weak transcription	Left Ventricle	heart
28	chr13:40138600-40139600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr13:40138600-40140400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:40138600-40140400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:40138600-40140400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr13:40138600-40140400	Enhancers	Adipose Nuclei	Adipose
33	chr13:40138800-40139600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:40138800-40139800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:40138800-40139800	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:40138800-40139800	Enhancers	Brain Substantia Nigra	brain
37	chr13:40138800-40139800	Flanking Active TSS	NHDF-Ad	bronchial
38	chr13:40138800-40140000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr13:40138800-40140400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:40138800-40141600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:40138800-40152800	Weak transcription	Aorta	Aorta
42	chr13:40139000-40140200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:40139000-40140400	Active TSS	A549	lung
44	chr13:40139000-40140400	Enhancers	HUVEC	blood vessel
45	chr13:40139000-40140600	Enhancers	Brain Anterior Caudate	brain
46	chr13:40139000-40140600	Enhancers	Fetal Lung	lung
47	chr13:40139200-40139600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr13:40139200-40139600	Active TSS	NHLF	lung
49	chr13:40139200-40139800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr13:40139200-40139800	Enhancers	Fetal Brain Female	brain

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