Variant report

Variant	rs2416549
Chromosome Location	chr12:11325804-11325805
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	POLR2A	chr12:11325704-11325881	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:11325789-11326363	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:11325711..11328028-chr12:11332674..11335077,2	K562	blood:
2	chr12:11322782..11326787-chr12:11332516..11335699,5	K562	blood:
3	chr12:11321748..11327565-chr12:11327784..11333912,14	MCF-7	breast:

Variant related genes	Relation type
TAS2R14	TF binding region
PRR4	TF binding region
ENSG00000256712	TF binding region
ENSG00000256629	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1047709	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1047712	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11557132	0.81[ASN][1000 genomes]
rs1349553	0.87[ASN][1000 genomes]
rs1451766	0.95[ASN][1000 genomes]
rs1451774	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551193	0.87[ASN][1000 genomes]
rs17817150	0.95[ASN][1000 genomes]
rs1863848	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123006	0.82[ASN][1000 genomes]
rs2123007	0.82[ASN][1000 genomes]
rs2167481	0.82[ASN][1000 genomes]
rs2290318	0.87[ASN][1000 genomes]
rs2290319	0.87[ASN][1000 genomes]
rs2416544	0.82[ASN][1000 genomes]
rs2416545	0.82[ASN][1000 genomes]
rs2416546	0.82[ASN][1000 genomes]
rs2416547	0.82[ASN][1000 genomes]
rs2416548	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34018339	0.82[ASN][1000 genomes]
rs34134804	0.95[ASN][1000 genomes]
rs34270405	0.82[ASN][1000 genomes]
rs34272839	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34373518	0.86[ASN][1000 genomes]
rs34413287	0.95[ASN][1000 genomes]
rs34531956	0.82[ASN][1000 genomes]
rs34648613	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34666803	0.87[ASN][1000 genomes]
rs34708147	0.83[ASN][1000 genomes]
rs34949195	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35151793	0.82[ASN][1000 genomes]
rs35499317	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35650731	0.95[ASN][1000 genomes]
rs35746980	0.87[ASN][1000 genomes]
rs35969491	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3863325	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3911234	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3911800	0.83[ASN][1000 genomes]
rs4101885	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4583064	0.99[ASN][1000 genomes]
rs5020531	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61928618	0.82[ASN][1000 genomes]
rs61928619	0.82[ASN][1000 genomes]
rs61928642	0.82[ASN][1000 genomes]
rs61928643	0.82[ASN][1000 genomes]
rs6488346	0.86[ASN][1000 genomes]
rs6488357	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6488358	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67471783	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67955183	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67961444	0.80[ASN][1000 genomes]
rs7132674	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7136602	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71453440	0.95[ASN][1000 genomes]
rs7302711	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316032	0.86[ASN][1000 genomes]
rs7350611	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7488095	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488102	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969625	0.82[ASN][1000 genomes]
rs7976950	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980677	0.83[ASN][1000 genomes]
rs8300	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv1042134	chr12:11220712-11328131	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs2416549	TAS2R14	cis	Nerve Tibial	GTEx
rs2416549	RP11-434C1.1	cis	Artery Aorta	GTEx
rs2416549	TAS2R14	cis	Thyroid	GTEx
rs2416549	PRR4	cis	Thyroid	GTEx
rs2416549	RP11-434C1.1	cis	Stomach	GTEx
rs2416549	TAS2R20	cis	Nerve Tibial	GTEx
rs2416549	TAS2R14	cis	Skin Sun Exposed Lower leg	GTEx
rs2416549	RP11-434C1.1	cis	Heart Left Ventricle	GTEx
rs2416549	TAS2R20	cis	Adipose Subcutaneous	GTEx
rs2416549	TAS2R14	cis	Muscle Skeletal	GTEx
rs2416549	TAS2R20	cis	lung	GTEx
rs2416549	RP11-785H5.1	cis	Muscle Skeletal	GTEx
rs2416549	RP11-434C1.1	cis	Whole Blood	GTEx
rs2416549	RP11-434C1.1	cis	Esophagus Muscularis	GTEx
rs2416549	RP11-434C1.1	cis	Esophagus Mucosa	GTEx
rs2416549	PRR4	cis	Heart Left Ventricle	GTEx
rs2416549	PRR4	cis	lung	GTEx
rs2416549	PRR4	cis	Adipose Subcutaneous	GTEx
rs2416549	TAS2R14	cis	Esophagus Muscularis	GTEx
rs2416549	TAS2R14	cis	lung	GTEx
rs2416549	RP11-434C1.1	cis	Artery Tibial	GTEx
rs2416549	TAS2R20	cis	Thyroid	GTEx
rs2416549	RP11-434C1.1	cis	Muscle Skeletal	GTEx
rs2416549	PRR4	cis	Whole Blood	GTEx
rs2416549	RP11-434C1.1	cis	Thyroid	GTEx
rs2416549	RP11-434C1.1	cis	lung	GTEx
rs2416549	PRR4	cis	Artery Tibial	GTEx
rs2416549	PRR4	cis	multi-tissue	Pritchard
rs2416549	TAS2R20	cis	Skin Sun Exposed Lower leg	GTEx
rs2416549	RP11-434C1.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2416549	TAS2R14	cis	Artery Tibial	GTEx
rs2416549	TAS2R20	cis	Esophagus Mucosa	GTEx
rs2416549	TAS2R20	cis	Artery Tibial	GTEx
rs2416549	RP11-434C1.1	cis	Nerve Tibial	GTEx
rs2416549	TAS2R14	cis	Esophagus Mucosa	GTEx
rs2416549	TAS2R14	cis	Adipose Subcutaneous	GTEx
rs2416549	RP11-434C1.1	cis	Adipose Subcutaneous	GTEx
rs2416549	PRR4	cis	Muscle Skeletal	GTEx
rs2416549	PRR4	cis	Esophagus Muscularis	GTEx
rs2416549	TAS2R20	cis	Esophagus Muscularis	GTEx
rs2416549	TAS2R20	cis	Muscle Skeletal	GTEx
rs2416549	PRR4	cis	Nerve Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11322200-11326000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:11322800-11326200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:11323400-11326000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:11323400-11326000	Active TSS	Muscle Satellite Cultured Cells	--
5	chr12:11323400-11326000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:11323600-11326200	Active TSS	Ovary	ovary
7	chr12:11324200-11326000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:11324200-11326200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:11324600-11326000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:11324800-11326600	Weak transcription	Esophagus	oesophagus
11	chr12:11325000-11326000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:11325000-11326200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:11325000-11335600	Weak transcription	Left Ventricle	heart
14	chr12:11325200-11326000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:11325200-11326000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:11325200-11326000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:11325200-11326000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:11325200-11326000	Enhancers	Colon Smooth Muscle	Colon
19	chr12:11325200-11326200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:11325200-11326200	Enhancers	Adipose Nuclei	Adipose
21	chr12:11325200-11326200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:11325200-11326400	Enhancers	Fetal Heart	heart
23	chr12:11325200-11327000	Enhancers	Brain Substantia Nigra	brain
24	chr12:11325200-11327800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:11325200-11328400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:11325200-11328600	Weak transcription	Thymus	Thymus
27	chr12:11325200-11330000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:11325200-11330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:11325200-11332200	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:11325200-11332200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:11325400-11326000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:11325400-11326000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:11325400-11326000	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:11325400-11326000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr12:11325400-11326000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:11325400-11326000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:11325400-11326000	Enhancers	Brain Anterior Caudate	brain
38	chr12:11325400-11326000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:11325400-11326000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr12:11325400-11326000	Enhancers	Hela-S3	cervix
41	chr12:11325400-11326000	Transcr. at gene 5' and 3'	HSMM	muscle
42	chr12:11325400-11326000	Flanking Active TSS	NHEK	skin
43	chr12:11325400-11326200	Enhancers	Brain Hippocampus Middle	brain
44	chr12:11325400-11326200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr12:11325400-11326400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:11325400-11331400	Weak transcription	Psoas Muscle	Psoas
47	chr12:11325400-11331800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:11325400-11332000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:11325600-11326000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:11325600-11326000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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