Variant report

Variant	rs12424233
Chromosome Location	chr12:120800543-120800544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr12:120798645-120800948	SK-N-SH	brain:	n/a	chr12:120799690-120799704 chr12:120799697-120799706 chr12:120799692-120799707 chr12:120799689-120799704 chr12:120799691-120799708 chr12:120799695-120799709 chr12:120799692-120799707 chr12:120799357-120799372 chr12:120799693-120799702 chr12:120799692-120799707 chr12:120799357-120799372 chr12:120800331-120800339 chr12:120799357-120799372
2	ZNF263	chr12:120800423-120800723	HEK293-T-REx	kidney:	n/a	chr12:120800567-120800588
3	REST	chr12:120798813-120800796	H1-neurons	neurons:	n/a	chr12:120799888-120799908 chr12:120799932-120799945 chr12:120800492-120800505 chr12:120799711-120799724 chr12:120798991-120798999 chr12:120799810-120799823

No.	Distal block	Cell Line	Cell type
1	chr12:120799434..120804968-chr12:120812300..120816168,6	K562	blood:
2	chr12:120800502..120802375-chr12:120882088..120884770,2	MCF-7	breast:
3	chr12:120728315..120730053-chr12:120799765..120801702,2	MCF-7	breast:
4	chr12:120799433..120803407-chr12:120804628..120808209,5	K562	blood:

Variant related genes	Relation type
MSI1	TF binding region
ENSG00000239881	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000257218	Chromatin interaction
ENSG00000135097	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12299143	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12423303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12424555	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12425936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427069	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12427095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16950044	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes]
rs16950047	0.82[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs16950058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16950061	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16950065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16950101	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238158	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238161	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239207	1.00[MKK][hapmap]
rs2464296	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2522140	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2701643	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2905543	0.80[EUR][1000 genomes]
rs3847967	1.00[CEU][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3847968	0.82[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs3847969	0.95[EUR][1000 genomes]
rs3898618	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56237802	0.93[ASN][1000 genomes]
rs5634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56733641	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57141366	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279831	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57384430	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58232894	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59447311	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59768240	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60176939	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60731947	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61140476	0.83[EUR][1000 genomes]
rs61592165	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61665022	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61748115	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7960401	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7977875	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9657936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657937	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9657948	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers 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	436 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12424233	SIRT4	cis	lymphoblastoid	seeQTL
rs12424233	SIRT4	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:120795800-120804200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:120796200-120805000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:120798400-120801600	Enhancers	Fetal Brain Male	brain
6	chr12:120799000-120800600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr12:120799000-120800600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:120799000-120800600	Enhancers	Fetal Heart	heart
9	chr12:120799000-120800800	Enhancers	Stomach Mucosa	stomach
10	chr12:120799000-120801200	Enhancers	Pancreas	Pancrea
11	chr12:120799600-120804000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:120799600-120804200	Weak transcription	Left Ventricle	heart
13	chr12:120799800-120800600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:120799800-120800600	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr12:120799800-120800800	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:120800000-120800600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:120800000-120800800	Enhancers	Brain Angular Gyrus	brain
18	chr12:120800000-120800800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr12:120800000-120801200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:120800000-120801200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:120800000-120801400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:120800000-120801800	Enhancers	Fetal Muscle Leg	muscle
23	chr12:120800000-120802200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:120800000-120805000	Enhancers	Fetal Intestine Large	intestine
25	chr12:120800200-120800600	Genic enhancers	H9 Cell Line	embryonic stem cell
26	chr12:120800200-120800600	Genic enhancers	Right Ventricle	heart
27	chr12:120800200-120800800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr12:120800200-120800800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:120800200-120800800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
30	chr12:120800200-120800800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:120800200-120800800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:120800200-120800800	Enhancers	Brain Substantia Nigra	brain
33	chr12:120800200-120801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:120800200-120801000	Genic enhancers	Fetal Lung	lung
35	chr12:120800200-120801000	Genic enhancers	Fetal Stomach	stomach
36	chr12:120800200-120801200	Enhancers	Gastric	stomach
37	chr12:120800200-120801400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr12:120800200-120801600	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:120800200-120802200	Genic enhancers	H1 Cell Line	embryonic stem cell
40	chr12:120800200-120802600	Enhancers	Brain Anterior Caudate	brain
41	chr12:120800200-120803400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:120800200-120804000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:120800200-120804000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:120800200-120805200	Genic enhancers	Fetal Intestine Small	intestine
45	chr12:120800200-120805400	Weak transcription	Ovary	ovary
46	chr12:120800400-120800600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
47	chr12:120800400-120800800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr12:120800400-120801200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:120800400-120801400	Enhancers	Brain Hippocampus Middle	brain
50	chr12:120800400-120801800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell

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