Variant report

Variant	rs6075948
Chromosome Location	chr20:22746255-22746256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1761	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092660	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143902	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179856	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179859	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2404493	0.95[EUR][1000 genomes]
rs2424461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424464	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424465	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424466	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424468	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424473	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424475	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2424476	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4331580	0.95[EUR][1000 genomes]
rs4516506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815144	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6075947	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6082814	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6113803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6113810	0.95[EUR][1000 genomes]

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	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6075948	CST3	cis	lymphoblastoid	seeQTL
rs6075948	THBD	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22737800-22749000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:22743200-22746600	Enhancers	Fetal Muscle Leg	muscle
3	chr20:22743200-22751400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:22744000-22748800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:22744600-22749000	Weak transcription	NH-A	brain
6	chr20:22744600-22749200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr20:22744800-22748800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:22745200-22749400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:22745400-22750800	Weak transcription	Hela-S3	cervix
10	chr20:22745400-22752400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:22745400-22752400	Weak transcription	Gastric	stomach
12	chr20:22745600-22749000	Weak transcription	HSMMtube	muscle
13	chr20:22745800-22747000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:22745800-22748000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr20:22745800-22748200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr20:22745800-22748600	Weak transcription	HSMM	muscle
17	chr20:22745800-22749400	Weak transcription	Stomach Mucosa	stomach
18	chr20:22746000-22747800	Weak transcription	Placenta	Placenta
19	chr20:22746000-22748800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:22746000-22748800	Weak transcription	A549	lung
21	chr20:22746000-22749000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:22746000-22749000	Weak transcription	Ovary	ovary
23	chr20:22746000-22749000	Weak transcription	HMEC	breast
24	chr20:22746000-22749200	Weak transcription	NHEK	skin
25	chr20:22746000-22749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:22746000-22751000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr20:22746000-22756000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links