Variant report

Variant	rs56346369
Chromosome Location	chr3:87038247-87038248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17028628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898266	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898268	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1946747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55854261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56077607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56781488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57070008	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57383190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57543641	0.96[ASN][1000 genomes]
rs57604593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59090592	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59701679	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61594756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551256	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6762893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784668	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802660	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916057	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72916059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72916081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916091	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916098	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916100	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918108	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918116	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72918121	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918124	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918169	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73844420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73844421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73844432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73844434	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73844442	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73844457	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617401	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627441	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649313	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959081	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87007200-87038400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:87016200-87039000	Weak transcription	Fetal Stomach	stomach
3	chr3:87017600-87039000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:87031600-87039600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:87032800-87039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:87032800-87039200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:87033000-87041000	Active TSS	Placenta	Placenta
8	chr3:87033800-87041200	Active TSS	HSMMtube	muscle
9	chr3:87034800-87040600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:87035400-87041000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:87035600-87040600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:87035800-87041200	Active TSS	Ovary	ovary
13	chr3:87035800-87041400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:87036200-87038800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:87036200-87038800	Active TSS	Fetal Muscle Leg	muscle
16	chr3:87036200-87041000	Active TSS	Right Atrium	heart
17	chr3:87036800-87038400	Weak transcription	Psoas Muscle	Psoas
18	chr3:87036800-87038600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:87036800-87040600	Active TSS	NHLF	lung
20	chr3:87037000-87041000	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr3:87037000-87041200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:87037200-87040600	Active TSS	Placenta Amnion	Placenta Amnion
23	chr3:87037200-87040800	Active TSS	HSMM	muscle
24	chr3:87037200-87041000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:87037400-87039400	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:87037400-87040600	Active TSS	Osteobl	bone
27	chr3:87037400-87040800	Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:87037600-87039000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:87037600-87039000	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:87037600-87039000	Active TSS	HMEC	breast
31	chr3:87037600-87039400	Active TSS	Adipose Nuclei	Adipose
32	chr3:87037600-87040800	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr3:87037600-87040800	Active TSS	Hela-S3	cervix
34	chr3:87037600-87041200	Active TSS	Fetal Lung	lung
35	chr3:87038000-87039200	Flanking Active TSS	HUVEC	blood vessel
36	chr3:87038000-87039400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:87038000-87041000	Active TSS	Aorta	Aorta
38	chr3:87038200-87038400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:87038200-87038600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:87038200-87038600	Flanking Active TSS	A549	lung
41	chr3:87038200-87038600	Flanking Active TSS	NH-A	brain
42	chr3:87038200-87038600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
43	chr3:87038200-87039000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:87038200-87039800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:87038200-87041000	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links