Variant report

Variant	rs12423303
Chromosome Location	chr12:120785685-120785686
allele	A/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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120783550..120785982-chr12:120791651..120794210,2	MCF-7	breast:
2	chr12:120783852..120785981-chr12:120787745..120789387,2	MCF-7	breast:
3	chr12:120784433..120787362-chr12:120891914..120893925,2	MCF-7	breast:
4	chr12:120783705..120785744-chr12:120882928..120885099,2	MCF-7	breast:
5	chr12:120637775..120640310-chr12:120783756..120785688,2	MCF-7	breast:
6	chr12:120729823..120732563-chr12:120784702..120787177,2	K562	blood:
7	chr12:120784911..120786735-chr12:120900322..120901993,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170855	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000257218	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11065147	1.00[YRI][hapmap]
rs11065157	1.00[YRI][hapmap]
rs1151845	1.00[YRI][hapmap]
rs1167699	1.00[YRI][hapmap]
rs1167706	1.00[YRI][hapmap]
rs12299143	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12424233	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	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12425936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427069	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12427095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16950044	0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs16950047	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs16950058	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950061	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950101	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1710142	1.00[YRI][hapmap]
rs1710146	1.00[YRI][hapmap]
rs2238158	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238161	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2464296	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2522140	0.93[EUR][1000 genomes]
rs2701643	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847967	0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap]
rs3847968	0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs3847969	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3847971	1.00[YRI][hapmap]
rs3898618	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767899	1.00[YRI][hapmap]
rs542407	1.00[YRI][hapmap]
rs56237802	0.88[ASN][1000 genomes]
rs5634	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56733641	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57141366	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57279831	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57384430	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58232894	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59447311	0.88[EUR][1000 genomes]
rs59768240	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60176939	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs606443	1.00[YRI][hapmap]
rs60731947	0.98[EUR][1000 genomes]
rs61592165	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61665022	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61748115	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs667913	1.00[YRI][hapmap]
rs671566	1.00[YRI][hapmap]
rs787818	1.00[YRI][hapmap]
rs787828	1.00[YRI][hapmap]
rs7960401	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7977875	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9657936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657937	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9657941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657942	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657948	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[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
rs12423303	SIRT4	cis	lymphoblastoid	seeQTL
rs12423303	SIRT4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120764000-120799200	Weak transcription	Right Atrium	heart
2	chr12:120776000-120793200	Weak transcription	Fetal Brain Male	brain
3	chr12:120778600-120794600	Weak transcription	Brain Anterior Caudate	brain
4	chr12:120779200-120794600	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:120779400-120796800	Strong transcription	Brain Germinal Matrix	brain
6	chr12:120779600-120799000	Weak transcription	Fetal Heart	heart
7	chr12:120779800-120794600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:120779800-120797400	Strong transcription	Fetal Brain Female	brain
9	chr12:120779800-120798800	Strong transcription	Fetal Intestine Small	intestine
10	chr12:120780000-120786200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:120780200-120787400	Weak transcription	Pancreas	Pancrea
12	chr12:120780200-120794600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:120780400-120787400	Weak transcription	Liver	Liver
14	chr12:120780400-120797600	Strong transcription	Fetal Stomach	stomach
15	chr12:120780800-120788800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:120780800-120792200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:120781000-120794200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:120781000-120794600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:120781000-120794600	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:120781000-120796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:120781000-120796200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:120781000-120796800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:120781200-120786400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:120781200-120794600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:120781200-120796000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:120781200-120796600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:120781200-120796800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:120781400-120796600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:120781600-120794600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:120781800-120794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:120781800-120794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:120782000-120790200	Weak transcription	Fetal Kidney	kidney
34	chr12:120783200-120786200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:120783200-120786200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr12:120783400-120794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:120783600-120786400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:120783600-120794600	Weak transcription	Brain Angular Gyrus	brain
39	chr12:120783800-120785800	Strong transcription	Right Ventricle	heart
40	chr12:120783800-120794200	Weak transcription	Brain Substantia Nigra	brain
41	chr12:120783800-120799000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:120784200-120786000	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr12:120784400-120786800	Strong transcription	Fetal Intestine Large	intestine
44	chr12:120784600-120788400	Weak transcription	Ovary	ovary
45	chr12:120784800-120800400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:120785000-120786000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:120785000-120786000	Strong transcription	Fetal Lung	lung
48	chr12:120785000-120786000	Genic enhancers	Gastric	stomach
49	chr12:120785000-120786800	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:120785200-120785800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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