Variant report

Variant	rs3898618
Chromosome Location	chr12:120813921-120813922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120807905..120811121-chr12:120812989..120814998,3	K562	blood:
2	chr12:120808109..120810194-chr12:120813483..120815462,2	MCF-7	breast:
3	chr12:120799434..120804968-chr12:120812300..120816168,6	K562	blood:
4	chr12:120812502..120815331-chr12:120816512..120818063,2	K562	blood:
5	chr12:120813114..120815441-chr12:120875563..120877352,2	MCF-7	breast:
6	chr12:120801365..120804968-chr12:120812471..120817033,4	K562	blood:

Variant related genes	Relation type
ENSG00000111780	Chromatin interaction
ENSG00000239881	Chromatin interaction
ENSG00000111775	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12299143	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12423303	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12424233	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12424555	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12425936	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12426900	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12427069	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12427095	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16950044	0.93[EUR][1000 genomes]
rs16950047	0.93[EUR][1000 genomes]
rs16950058	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16950061	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16950065	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16950101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238158	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238161	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2464296	0.95[EUR][1000 genomes]
rs2522140	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2701643	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2905543	0.80[EUR][1000 genomes]
rs3847967	0.81[EUR][1000 genomes]
rs3847968	0.95[EUR][1000 genomes]
rs3847969	0.95[EUR][1000 genomes]
rs56237802	0.93[ASN][1000 genomes]
rs5634	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56733641	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57141366	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57279831	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57384430	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58232894	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59447311	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59768240	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60176939	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60731947	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61140476	0.83[EUR][1000 genomes]
rs61592165	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61665022	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61748115	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7960401	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7977875	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9657936	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9657937	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9657941	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9657942	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9657948	0.82[AMR][1000 genomes];1.00[EUR][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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3898618	SIRT4	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120807800-120814000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:120809400-120814000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:120811800-120814400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:120813200-120814800	Bivalent Enhancer	HepG2	liver
5	chr12:120813200-120815600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:120813600-120815000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:120813600-120815200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr12:120813600-120815400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:120813600-120815600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:120813600-120815600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr12:120813600-120815600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:120813600-120815600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:120813800-120814000	Enhancers	A549	lung
14	chr12:120813800-120814000	Enhancers	Hela-S3	cervix
15	chr12:120813800-120814000	Bivalent Enhancer	NH-A	brain
16	chr12:120813800-120814600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:120813800-120814600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:120813800-120814600	Enhancers	HMEC	breast
19	chr12:120813800-120815000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:120813800-120815000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:120813800-120815400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:120813800-120815600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:120813800-120815800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:120813800-120819200	Weak transcription	Fetal Intestine Small	intestine

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