Variant report

Variant	rs4147672
Chromosome Location	chr12:4764137-4764138
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	JUND	chr12:4763890-4764208	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:4754845..4760714-chr12:4761830..4765057,7	MCF-7	breast:
2	chr12:4756861..4759668-chr12:4760395..4765208,7	MCF-7	breast:
3	chr12:4757573..4759938-chr12:4760465..4764276,3	K562	blood:
4	chr12:4762857..4765662-chr12:4767685..4769794,2	K562	blood:
5	chr12:4762342..4764303-chr12:4764418..4767058,2	K562	blood:

Variant related genes	Relation type
NDUFA9	TF binding region
ENSG00000255639	TF binding region
ENSG00000139180	Chromatin interaction
ENSG00000111254	Chromatin interaction
ENSG00000255639	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11063280	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063282	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063285	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614014	0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs11614030	1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12303320	0.85[ASN][1000 genomes]
rs12308883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309713	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310639	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12313377	0.87[ASN][1000 genomes]
rs12318966	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12811453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828416	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs12829711	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs16931616	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16931620	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860343	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs1990311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072354	0.80[EUR][1000 genomes]
rs2267548	0.90[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299833	0.86[ASN][1000 genomes]
rs2302246	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35131771	0.82[ASN][1000 genomes]
rs35167443	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147666	0.90[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4147667	0.83[TSI][hapmap]
rs4147671	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147673	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147678	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147679	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147680	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147682	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147684	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147685	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766264	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4766267	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4766269	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61909965	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136668	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs7312402	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958182	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972657	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972737	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs7972920	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975484	0.82[ASN][1000 genomes]
rs7977981	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs876586	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv898617	chr12:4715082-4768619	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898618	chr12:4726068-4764137	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898619	chr12:4737715-4771456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv898620	chr12:4745313-4771456	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv557125	chr12:4748410-4764137	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036308	chr12:4748657-4804156	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv898621	chr12:4751798-4768193	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv898622	chr12:4751798-4768619	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv898623	chr12:4751798-4771456	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
11	nsv898624	chr12:4757474-4769876	Weak transcription Strong transcription Flanking Active TSS Enhancers 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	5 gene(s)	inside rSNPs	diseases
12	nsv557126	chr12:4757809-4768619	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv898625	chr12:4759380-4771682	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4147672	AKAP3	cis	Thyroid	GTEx
rs4147672	AKAP3	cis	parietal	SCAN
rs4147672	ACRBP	cis	parietal	SCAN
rs4147672	DYRK4	Cis_1M	lymphoblastoid	RTeQTL
rs4147672	AKAP3	cis	cerebellum	SCAN
rs4147672	SCNN1A	cis	cerebellum	SCAN
rs4147672	NDUFA9	cis	parietal	SCAN
rs4147672	ADIPOR2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4759000-4764200	Weak transcription	Esophagus	oesophagus
2	chr12:4759000-4764400	Weak transcription	Aorta	Aorta
3	chr12:4759000-4764400	Weak transcription	Pancreas	Pancrea
4	chr12:4759000-4772600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:4759000-4799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:4759200-4764400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:4759200-4776200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:4759400-4764800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:4759400-4767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:4759600-4764400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:4759600-4764800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:4759600-4767000	Weak transcription	Stomach Mucosa	stomach
13	chr12:4759800-4764200	Weak transcription	NHLF	lung
14	chr12:4760000-4764200	Weak transcription	Gastric	stomach
15	chr12:4760000-4766600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:4760000-4766600	Weak transcription	Fetal Brain Male	brain
17	chr12:4760200-4765000	Weak transcription	Psoas Muscle	Psoas
18	chr12:4760800-4782400	Strong transcription	Primary T cells from cord blood	blood
19	chr12:4761200-4765600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:4761800-4782200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:4762200-4779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:4762200-4783600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:4762600-4768800	Weak transcription	Fetal Heart	heart
24	chr12:4762600-4773000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:4762600-4773400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:4762600-4779600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:4762600-4780000	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:4762600-4782800	Strong transcription	Adipose Nuclei	Adipose
29	chr12:4762800-4779800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:4762800-4781000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:4762800-4782000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:4763000-4766600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:4763000-4774800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:4763000-4775600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:4763000-4780400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:4763000-4782200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:4763000-4782400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:4763000-4782400	Strong transcription	Placenta	Placenta
39	chr12:4763000-4783000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:4763200-4772600	Strong transcription	HSMM	muscle
41	chr12:4763200-4772600	Strong transcription	Osteobl	bone
42	chr12:4763200-4773600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:4763200-4782200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:4763400-4764600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:4763400-4764600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:4763400-4764600	Strong transcription	Hela-S3	cervix
47	chr12:4763400-4765000	Strong transcription	Brain Angular Gyrus	brain
48	chr12:4763400-4766000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:4763400-4771200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:4763400-4771200	Strong transcription	Fetal Stomach	stomach

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