Variant report

Variant	rs4634948
Chromosome Location	chr1:56291165-56291166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs4244649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384273	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4433442	0.87[CEU][hapmap]
rs4497258	1.00[ASN][1000 genomes]
rs4503390	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512692	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927271	1.00[ASN][1000 genomes]
rs6588577	1.00[ASN][1000 genomes]
rs6662329	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349129	1.00[ASN][1000 genomes]
rs7549387	0.82[AFR][1000 genomes];1.00[EUR][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	nsv829926	chr1:56188492-56360745	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv1002958	chr1:56278696-56295112	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4634948	ZSWIM1	trans	lymphoblastoid	RTeQTL
rs4634948	GLIS1	cis	parietal	SCAN
rs4634948	ACOT11	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56283000-56293000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:56283200-56292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:56288000-56292000	Enhancers	Fetal Lung	lung
4	chr1:56289400-56292800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:56289600-56292000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:56289600-56292000	Weak transcription	Fetal Stomach	stomach
7	chr1:56289600-56292400	Weak transcription	Osteobl	bone
8	chr1:56289800-56291200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:56289800-56291200	Weak transcription	Placenta	Placenta
10	chr1:56289800-56292000	Weak transcription	HSMMtube	muscle
11	chr1:56289800-56292200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:56289800-56292400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:56289800-56292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:56289800-56293000	Weak transcription	NH-A	brain
15	chr1:56290200-56291200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:56290600-56291400	Enhancers	Fetal Kidney	kidney
17	chr1:56290800-56293000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:56290800-56293800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:56290800-56294000	Enhancers	NHDF-Ad	bronchial
20	chr1:56290800-56294200	Enhancers	NHLF	lung
21	chr1:56291000-56292600	Enhancers	Colon Smooth Muscle	Colon

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