Variant report

Variant	rs2238158
Chromosome Location	chr12:120781746-120781747
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120759487..120761384-chr12:120780386..120782433,2	MCF-7	breast:
2	chr12:120728324..120731072-chr12:120780258..120783965,5	MCF-7	breast:
3	chr12:120728241..120730871-chr12:120781160..120783307,2	K562	blood:
4	chr12:120729551..120732306-chr12:120778974..120781933,2	MCF-7	breast:
5	chr12:120636613..120638963-chr12:120780314..120783183,3	MCF-7	breast:
6	chr12:120780232..120784362-chr12:120789463..120792273,4	K562	blood:
7	chr12:120779310..120781400-chr12:120781688..120783455,2	MCF-7	breast:
8	chr12:120779682..120782065-chr12:120783234..120785150,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12299143	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423303	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12424233	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12424555	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12425936	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426900	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427069	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12427095	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950044	0.86[EUR][1000 genomes]
rs16950047	0.86[EUR][1000 genomes]
rs16950058	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950061	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950065	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950101	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2238161	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2464296	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2522140	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2701643	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847968	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3847969	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3898618	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56237802	0.91[ASN][1000 genomes]
rs5634	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56733641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57141366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57279831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57384430	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58232894	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59447311	0.90[EUR][1000 genomes]
rs59768240	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60176939	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60731947	1.00[EUR][1000 genomes]
rs61592165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61665022	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61748115	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7960401	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7977875	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9657936	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657937	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9657941	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657942	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657948	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2238158	SIRT4	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120764000-120783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:120764000-120799200	Weak transcription	Right Atrium	heart
3	chr12:120769400-120785000	Weak transcription	Gastric	stomach
4	chr12:120776000-120793200	Weak transcription	Fetal Brain Male	brain
5	chr12:120776400-120781800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120776600-120784200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:120778600-120794600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:120779200-120794600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:120779400-120796800	Strong transcription	Brain Germinal Matrix	brain
10	chr12:120779600-120783200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:120779600-120799000	Weak transcription	Fetal Heart	heart
12	chr12:120779800-120794600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:120779800-120797400	Strong transcription	Fetal Brain Female	brain
14	chr12:120779800-120798800	Strong transcription	Fetal Intestine Small	intestine
15	chr12:120780000-120783800	Weak transcription	Right Ventricle	heart
16	chr12:120780000-120786200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:120780200-120784400	Weak transcription	Fetal Intestine Large	intestine
18	chr12:120780200-120785000	Weak transcription	Fetal Lung	lung
19	chr12:120780200-120787400	Weak transcription	Pancreas	Pancrea
20	chr12:120780200-120794600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:120780400-120781800	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:120780400-120781800	Enhancers	HepG2	liver
23	chr12:120780400-120783200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:120780400-120787400	Weak transcription	Liver	Liver
25	chr12:120780400-120797600	Strong transcription	Fetal Stomach	stomach
26	chr12:120780800-120788800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:120780800-120792200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:120781000-120783200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:120781000-120784200	Weak transcription	Ovary	ovary
31	chr12:120781000-120794200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:120781000-120794600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:120781000-120794600	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:120781000-120796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:120781000-120796200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:120781000-120796800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:120781200-120781800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:120781200-120782200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:120781200-120786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:120781200-120794600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:120781200-120796000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:120781200-120796600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:120781200-120796800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:120781400-120783200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:120781400-120785000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:120781400-120796600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:120781600-120781800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:120781600-120785000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:120781600-120794600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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