Variant report

Variant	rs17111762
Chromosome Location	chr10:98141748-98141749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11188740	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11594430	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11597420	0.88[MEX][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs12252784	1.00[JPT][hapmap]
rs2093557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.90[ASN][1000 genomes]
rs2181324	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2273891	0.82[TSI][hapmap]
rs28438557	0.90[ASN][1000 genomes]
rs2901993	0.90[ASN][1000 genomes]
rs56094817	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1047657	chr10:98123234-98183487	Weak transcription Active TSS Genic enhancers Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17111762	GOT1	cis	cerebellum	SCAN
rs17111762	CHUK	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98135400-98149600	Weak transcription	Right Atrium	heart
2	chr10:98138200-98145000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:98138200-98146400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:98138800-98144200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:98138800-98144200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:98139400-98142400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:98139600-98141800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr10:98140000-98149200	Weak transcription	Gastric	stomach
9	chr10:98141400-98141800	Enhancers	Brain Germinal Matrix	brain
10	chr10:98141400-98142200	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:98141400-98142400	Weak transcription	Left Ventricle	heart
12	chr10:98141400-98146600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:98141400-98146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:98141400-98150200	Weak transcription	Spleen	Spleen

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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