Variant report

Variant	rs9870114
Chromosome Location	chr3:100970240-100970241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10936607	0.81[ASN][1000 genomes]
rs13087404	0.81[ASN][1000 genomes]
rs13089177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089552	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250611	0.81[ASN][1000 genomes]
rs2317699	0.81[ASN][1000 genomes]
rs2317700	0.80[ASN][1000 genomes]
rs2317745	0.81[ASN][1000 genomes]
rs2317749	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2317751	0.81[ASN][1000 genomes]
rs2433031	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2553416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2553424	0.80[ASN][1000 genomes]
rs2553427	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2553430	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682384	0.81[ASN][1000 genomes]
rs2682386	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2682390	0.81[ASN][1000 genomes]
rs2682391	0.81[ASN][1000 genomes]
rs348866	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348869	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683899	0.81[ASN][1000 genomes]
rs4683900	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs473702	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs487623	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs497953	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs503734	0.87[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs508537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs520558	0.81[ASN][1000 genomes]
rs533852	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs551442	0.81[ASN][1000 genomes]
rs56075912	0.81[ASN][1000 genomes]
rs62280667	0.81[ASN][1000 genomes]
rs6441602	0.81[ASN][1000 genomes]
rs6773536	0.81[ASN][1000 genomes]
rs9816469	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9859077	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2754039	chr3:100882310-100981310	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9870114	ZNF329	trans	multi-tissue	Pritchard
rs9870114	ZNF256	trans	multi-tissue	Pritchard
rs9870114	ZNF671	trans	multi-tissue	Pritchard
rs9870114	IMPG2	cis	parietal	SCAN
rs9870114	ZNF447	trans	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100954800-100992600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:100955000-100994000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:100958800-101012800	Weak transcription	Left Ventricle	heart
4	chr3:100960400-100971200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:100962800-100970800	Weak transcription	Aorta	Aorta
6	chr3:100963200-100972000	Weak transcription	Primary T cells from cord blood	blood
7	chr3:100963400-100971800	Weak transcription	HSMM	muscle
8	chr3:100967400-100971200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:100967800-100970800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:100968000-100970800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:100968000-100971400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:100968200-100971200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:100968200-100971400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:100968200-100971600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:100968200-100971800	Weak transcription	HSMMtube	muscle
16	chr3:100968200-100974600	Weak transcription	Fetal Lung	lung

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