Variant report

Variant	rs4658240
Chromosome Location	chr1:92066183-92066184
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10782970	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11164996	0.83[ASN][1000 genomes]
rs12023393	0.86[ASN][1000 genomes]
rs12023428	0.83[ASN][1000 genomes]
rs12027582	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031900	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12046806	0.83[ASN][1000 genomes]
rs12564910	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131493	0.83[ASN][1000 genomes]
rs1848436	0.96[EUR][1000 genomes]
rs4658242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799005	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681340	0.83[ASN][1000 genomes]
rs6685470	0.86[ASN][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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv946071	chr1:92060669-92067233	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4658240	ZNF644	cis	parietal	SCAN
rs4658240	UPK1B	trans	parietal	SCAN
rs4658240	TGFBR3	cis	parietal	SCAN
rs4658240	RPAP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92051800-92067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92055800-92076400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:92057200-92070400	Weak transcription	Psoas Muscle	Psoas
4	chr1:92059600-92066200	Weak transcription	Fetal Stomach	stomach
5	chr1:92059600-92067200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:92059800-92068800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:92060600-92067200	Weak transcription	Lung	lung
8	chr1:92060600-92070200	Weak transcription	Right Ventricle	heart
9	chr1:92060800-92066400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:92060800-92066400	Weak transcription	Right Atrium	heart
11	chr1:92060800-92067200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:92060800-92067600	Weak transcription	Left Ventricle	heart
13	chr1:92060800-92070200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:92061200-92070000	Weak transcription	Ovary	ovary
15	chr1:92062400-92074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:92063200-92067800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:92064000-92070000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:92064600-92066400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:92064800-92066400	Weak transcription	Placenta	Placenta
20	chr1:92065400-92068400	Enhancers	Fetal Heart	heart
21	chr1:92065800-92066200	Weak transcription	K562	blood
22	chr1:92066000-92069200	Enhancers	NHDF-Ad	bronchial

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