Variant report

Variant	rs3858097
Chromosome Location	chr9:94951819-94951820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94906898..94908988-chr9:94950032..94952563,2	K562	blood:
2	chr9:94912447..94914532-chr9:94951103..94952987,2	MCF-7	breast:
3	chr9:94939871..94945930-chr9:94946587..94952427,7	K562	blood:
4	chr9:94946143..94949635-chr9:94950432..94953895,3	K562	blood:

Variant related genes	Relation type
ENSG00000225511	Chromatin interaction
ENSG00000238996	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10119626	0.84[ASN][1000 genomes]
rs10992265	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10992266	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10992267	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12345822	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs15717	1.00[CHB][hapmap]
rs16908281	1.00[CHB][hapmap]
rs17518754	1.00[CHB][hapmap]
rs17678735	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs2236344	1.00[CHB][hapmap]
rs2236529	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs2273860	1.00[CHB][hapmap]
rs2274967	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs3736836	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs3737147	0.88[CHD][hapmap]
rs3758230	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs3780340	1.00[CHB][hapmap]
rs3780341	1.00[CHB][hapmap]
rs3780342	1.00[CHB][hapmap]
rs3889951	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4298540	1.00[CHB][hapmap]
rs7863859	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7872423	0.89[CHD][hapmap]
rs921122	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3858097	CENPP	cis	cerebellum	SCAN
rs3858097	CENPP	cis	Adipose Subcutaneous	GTEx
rs3858097	IARS	cis	lymphoblastoid	seeQTL
rs3858097	CENPP	cis	Muscle Skeletal	GTEx
rs3858097	IPPK	cis	cerebellum	SCAN
rs3858097	CENPP	cis	Esophagus Muscularis	GTEx
rs3858097	CENPP	cis	parietal	SCAN
rs3858097	CENPP	cis	Nerve Tibial	GTEx
rs3858097	CENPP	cis	Artery Tibial	GTEx
rs3858097	ZNF484	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94944800-94955800	Weak transcription	Right Atrium	heart
2	chr9:94949800-94952800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:94950600-94954400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:94951200-94952600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:94951200-94953000	Enhancers	Fetal Muscle Leg	muscle
6	chr9:94951400-94952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:94951400-94952200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr9:94951400-94952800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:94951600-94952200	Bivalent Enhancer	Fetal Stomach	stomach
10	chr9:94951600-94952600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:94951600-94952600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:94951600-94952800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:94951800-94952000	Bivalent Enhancer	Adipose Nuclei	Adipose
14	chr9:94951800-94952200	Active TSS	HepG2	liver
15	chr9:94951800-94952600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:94951800-94952800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:94951800-94953000	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links