Variant report

Variant	rs3742039
Chromosome Location	chr12:120649970-120649971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120646880..120656528-chr12:120726067..120732546,19	K562	blood:
2	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
3	chr12:120649749..120656129-chr12:120724644..120730997,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000123009	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10437836	0.83[ASN][1000 genomes]
rs10744748	0.81[JPT][hapmap]
rs11065035	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11065036	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs11065040	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1151824	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1151825	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1151827	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1151832	0.82[JPT][hapmap]
rs1151837	0.86[JPT][hapmap]
rs11836049	0.82[ASN][1000 genomes]
rs1183781	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs12310433	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12312562	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs12321884	0.81[ASN][1000 genomes]
rs1634814	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2074540	0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2238155	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239206	0.91[ASW][hapmap];0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2240312	0.83[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs2240317	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2240318	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2240321	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2240322	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2240323	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2240324	0.80[EUR][1000 genomes]
rs2240325	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2269941	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2269944	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2269945	0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2283362	0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2283364	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2286049	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2286050	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2286051	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2422	0.86[JPT][hapmap]
rs3888586	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7134706	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7296380	0.85[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs7310175	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7960120	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974732	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	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
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
7	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
8	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
rs3742039	SIRT4	cis	lymphoblastoid	seeQTL
rs3742039	GCN1L1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120639600-120651400	Weak transcription	Stomach Mucosa	stomach
2	chr12:120640000-120650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:120640000-120650200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:120640200-120651400	Weak transcription	Fetal Kidney	kidney
5	chr12:120640200-120661800	Weak transcription	GM12878-XiMat	blood
6	chr12:120640200-120662400	Weak transcription	Fetal Brain Male	brain
7	chr12:120640400-120651400	Weak transcription	Brain Angular Gyrus	brain
8	chr12:120640600-120651200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:120643800-120651400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:120643800-120652800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:120643800-120654000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:120643800-120654200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:120643800-120661800	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:120644000-120660400	Strong transcription	Fetal Intestine Small	intestine
15	chr12:120644000-120662600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:120644200-120654400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:120644200-120656600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:120644400-120654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:120644800-120661400	Strong transcription	Fetal Intestine Large	intestine
20	chr12:120645200-120654200	Strong transcription	A549	lung
21	chr12:120645800-120656600	Weak transcription	K562	blood
22	chr12:120646400-120662400	Weak transcription	Right Atrium	heart
23	chr12:120646800-120653000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:120647000-120650600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:120647000-120652400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:120647000-120652600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:120647000-120661400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:120647200-120654200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr12:120647200-120661400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:120647400-120651400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:120647400-120652800	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr12:120647400-120653200	Strong transcription	Fetal Brain Female	brain
33	chr12:120647400-120653200	Strong transcription	Fetal Thymus	thymus
34	chr12:120647400-120653200	Strong transcription	Dnd41	blood
35	chr12:120647400-120654400	Strong transcription	Primary T cells from cord blood	blood
36	chr12:120647400-120661600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr12:120647600-120650600	Strong transcription	HepG2	liver
38	chr12:120647600-120650600	Genic enhancers	NHEK	skin
39	chr12:120647600-120652400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:120647600-120652400	Strong transcription	Spleen	Spleen
41	chr12:120647600-120652600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:120647600-120652600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:120647600-120652600	Strong transcription	NH-A	brain
44	chr12:120647600-120652800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:120647600-120652800	Strong transcription	Brain Germinal Matrix	brain
46	chr12:120647600-120652800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr12:120647600-120652800	Strong transcription	Thymus	Thymus
48	chr12:120647600-120653000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:120647600-120653000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr12:120647600-120653000	Strong transcription	Placenta	Placenta

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