Variant report

Variant	rs2047478
Chromosome Location	chr12:62941929-62941930
allele	A/T
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	STAT3	chr12:62941867-62942111	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62936384..62938344-chr12:62940152..62942077,2	MCF-7	breast:
2	chr1:116960059..116961967-chr12:62941015..62944003,2	MCF-7	breast:
3	chr12:62939712..62942391-chr12:62948706..62950538,2	K562	blood:
4	chr12:62940703..62942604-chr12:62944482..62947077,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-399P	TF binding region
ENSG00000203865	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10128830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10128959	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10161549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219555	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10219765	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735907	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735909	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747963	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10747965	0.81[ASN][1000 genomes]
rs10747966	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784299	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784302	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784303	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784306	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877851	0.82[ASN][1000 genomes]
rs10877860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877863	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877865	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877866	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877868	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877869	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877872	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10877873	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877878	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877882	0.81[EUR][1000 genomes]
rs10877883	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877886	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877887	0.91[ASN][1000 genomes]
rs10877888	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs11174493	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11174497	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174507	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174520	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11174534	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11174538	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11174539	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174542	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174545	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11174550	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11495588	0.86[ASN][1000 genomes]
rs12227568	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305077	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12309683	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12371971	0.91[JPT][hapmap]
rs12371972	0.91[JPT][hapmap]
rs12578200	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12580048	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581171	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12809279	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12810119	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12829103	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498713	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2029937	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2047479	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141777	0.84[ASN][1000 genomes]
rs2220980	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35409044	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4763021	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4763174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763179	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4763180	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581452	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581454	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7134302	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136993	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71453871	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294404	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7298782	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302027	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308021	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7316612	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957417	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958597	0.83[ASN][1000 genomes]
rs7963657	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975183	0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7975560	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
2	chr12:62889200-62949600	Weak transcription	Small Intestine	intestine
3	chr12:62897600-62944000	Weak transcription	Esophagus	oesophagus
4	chr12:62903600-62949800	Weak transcription	NHEK	skin
5	chr12:62906400-62943800	Weak transcription	Aorta	Aorta
6	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:62911400-62944000	Weak transcription	Spleen	Spleen
8	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
10	chr12:62917400-62960000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:62920000-62950200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:62924400-62945600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr12:62924400-62949800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:62924800-62967600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:62925400-62949800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:62926000-62945000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:62926000-62951400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:62926200-62949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:62926200-62951400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:62926200-62951600	Strong transcription	Fetal Thymus	thymus
23	chr12:62926200-62951800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:62926200-62955800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:62927400-62967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:62927600-62943400	Weak transcription	HSMMtube	muscle
27	chr12:62928000-62942000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:62928000-62943400	Weak transcription	NHLF	lung
29	chr12:62928000-62950400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:62928000-62963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:62928200-62950000	Weak transcription	Fetal Brain Male	brain
32	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:62931800-62951400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:62932000-62947600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:62932000-62957200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:62932400-62946800	Weak transcription	K562	blood
37	chr12:62932400-62949800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:62932400-62949800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:62933800-62948200	Weak transcription	Lung	lung
40	chr12:62934600-62944400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:62934800-62955400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:62935000-62955200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:62935200-62945200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:62935400-62956400	Strong transcription	Placenta	Placenta
45	chr12:62935600-62955600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:62935800-62942000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:62936000-62955200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:62936200-62942400	Strong transcription	Adipose Nuclei	Adipose
49	chr12:62936200-62945600	Strong transcription	Fetal Lung	lung
50	chr12:62936200-62951200	Strong transcription	Fetal Muscle Trunk	muscle

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