Variant report

Variant	rs6729020
Chromosome Location	chr2:189064720-189064721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189060891..189062754-chr2:189063938..189066801,3	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10931334	0.83[AFR][1000 genomes]
rs10931336	0.83[AFR][1000 genomes]
rs13027011	0.81[AFR][1000 genomes]
rs4667213	0.83[AFR][1000 genomes]
rs6726013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6727856	0.92[EUR][1000 genomes]
rs6756267	0.92[EUR][1000 genomes]
rs73041652	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7582899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv875605	chr2:189017499-189080087	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6729020	TMSB15B	trans	brain	seeQTL
rs6729020	CLK4	trans	brain	seeQTL
rs6729020	TMEM52	trans	brain	seeQTL
rs6729020	TRIM3	trans	brain	seeQTL
rs6729020	TIMP4	trans	brain	seeQTL
rs6729020	MTNR1A	trans	brain	seeQTL
rs6729020	SFI1	trans	brain	seeQTL
rs6729020	CACNA1A	trans	brain	seeQTL
rs6729020	CHAD	trans	brain	seeQTL
rs6729020	EBF1	trans	brain	seeQTL
rs6729020	CD247	trans	brain	seeQTL
rs6729020	MDK	trans	brain	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189061600-189067400	Weak transcription	Ovary	ovary
2	chr2:189061800-189069200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:189062200-189065000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:189063200-189064800	Enhancers	NH-A	brain
5	chr2:189063600-189064800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:189063600-189065000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:189063600-189065200	Enhancers	Osteobl	bone
8	chr2:189063600-189065800	Enhancers	HMEC	breast
9	chr2:189063800-189065800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:189064000-189064800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:189064000-189064800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:189064000-189065200	Enhancers	HSMM	muscle
13	chr2:189064000-189065400	Enhancers	NHEK	skin
14	chr2:189064200-189065000	Enhancers	NHDF-Ad	bronchial
15	chr2:189064400-189064800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:189064400-189064800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:189064400-189064800	Enhancers	NHLF	lung
18	chr2:189064400-189065200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:189064400-189065200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:189064600-189064800	Enhancers	A549	lung
21	chr2:189064600-189065200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:189064600-189065400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links