Variant report

Variant	rs898548
Chromosome Location	chr10:44396631-44396632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10508874	0.99[ASN][1000 genomes]
rs10751347	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10751348	0.99[ASN][1000 genomes]
rs10899948	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1147900	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1147902	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254744	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254855	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254857	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254858	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254859	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1303233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1325487	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468060	0.80[ASN][1000 genomes]
rs1570847	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1749798	0.85[AMR][1000 genomes]
rs1749799	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1813245	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs1813897	0.94[ASN][1000 genomes]
rs2147875	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2147876	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169198	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274241	0.99[ASN][1000 genomes]
rs2798993	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4948787	0.99[ASN][1000 genomes]
rs4948789	0.98[ASN][1000 genomes]
rs7090750	0.99[ASN][1000 genomes]
rs7899385	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900414	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7915088	0.99[ASN][1000 genomes]
rs882902	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs883400	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912803	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9732790	0.99[ASN][1000 genomes]
rs984000	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051921	chr10:44378011-44458880	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs898548	ZNF239	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44388800-44397600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:44392400-44402000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:44394000-44397800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:44394200-44397600	Enhancers	Fetal Muscle Leg	muscle
5	chr10:44395000-44406200	Weak transcription	Esophagus	oesophagus
6	chr10:44395200-44397600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:44395200-44399000	Weak transcription	Right Ventricle	heart
8	chr10:44395200-44400000	Weak transcription	Fetal Heart	heart
9	chr10:44395200-44400000	Weak transcription	Left Ventricle	heart
10	chr10:44395200-44400200	Weak transcription	Fetal Kidney	kidney
11	chr10:44395400-44400400	Weak transcription	NHDF-Ad	bronchial
12	chr10:44395600-44397000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr10:44395800-44399800	Weak transcription	Adipose Nuclei	Adipose
14	chr10:44395800-44401400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr10:44396000-44399800	Weak transcription	Right Atrium	heart
16	chr10:44396000-44399800	Weak transcription	Spleen	Spleen
17	chr10:44396200-44397200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:44396400-44397200	Enhancers	Osteobl	bone
19	chr10:44396400-44401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:44396600-44399400	Enhancers	HepG2	liver

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