Variant report

Variant	rs12612549
Chromosome Location	chr2:64072747-64072748
allele	A/C
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	chr2:64066467-64077414	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:64072674-64072756	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr2:64067067-64074747	H1-hESC	embryonic stem cell:	n/a	chr2:64068850-64068860 chr2:64068822-64068832 chr2:64068878-64068888 chr2:64067996-64068006
4	SIN3A	chr2:64067165-64073428	H1-hESC	embryonic stem cell:	n/a	chr2:64073388-64073396
5	POLR2A	chr2:64072733-64073035	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:64072725-64073422	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:64072689-64073002	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF2	chr2:64072563-64073403	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF7	chr2:64067139-64075620	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64066407..64070482-chr2:64071096..64075382,10	MCF-7	breast:

Variant related genes	Relation type
UGP2	TF binding region
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10171008	0.81[ASN][1000 genomes]
rs10187013	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs10201844	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10207847	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10211360	0.84[CHB][hapmap]
rs10865343	0.84[CHB][hapmap]
rs11125985	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11125986	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12612596	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12613707	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12713497	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs12991311	0.85[CHB][hapmap]
rs13384707	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes]
rs1362797	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1440004	0.84[EUR][1000 genomes]
rs2054119	0.93[EUR][1000 genomes]
rs2080649	0.82[EUR][1000 genomes]
rs2165210	0.82[EUR][1000 genomes]
rs2302809	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2901636	0.83[EUR][1000 genomes]
rs329477	0.86[EUR][1000 genomes]
rs329480	0.84[CHB][hapmap]
rs329486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs36042418	0.91[EUR][1000 genomes]
rs3980405	0.82[EUR][1000 genomes]
rs4072113	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4293553	1.00[ASW][hapmap]
rs4318375	0.85[CHB][hapmap]
rs4359637	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4399712	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671526	0.85[EUR][1000 genomes]
rs4671528	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs4671532	0.92[EUR][1000 genomes]
rs6546025	0.95[CEU][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs6546026	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs6546027	0.93[EUR][1000 genomes]
rs6546038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546039	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546040	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546043	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs6546046	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs6705192	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6716322	0.83[EUR][1000 genomes]
rs6716558	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6727120	0.81[EUR][1000 genomes]
rs6737855	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6741298	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs6741584	0.84[CHB][hapmap]
rs6746875	0.84[EUR][1000 genomes]
rs6747307	0.84[CHB][hapmap]
rs6757168	0.81[ASN][1000 genomes]
rs7420396	0.81[ASN][1000 genomes]
rs7589241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7596262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602952	0.81[EUR][1000 genomes]
rs9309356	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs998043	0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers 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 miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64067000-64073200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:64067000-64075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:64067000-64076400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:64067200-64073200	Active TSS	Left Ventricle	heart
5	chr2:64067200-64073400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:64067400-64074000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:64067600-64072800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:64067600-64074000	Active TSS	Right Ventricle	heart
9	chr2:64069000-64072800	Weak transcription	Spleen	Spleen
10	chr2:64069400-64073400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr2:64069400-64074600	Transcr. at gene 5' and 3'	Dnd41	blood
12	chr2:64069800-64073200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
13	chr2:64070000-64073600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:64070000-64082800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:64070200-64076400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:64070200-64084600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:64070200-64103000	Weak transcription	Gastric	stomach
18	chr2:64070400-64075800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:64070600-64073000	Enhancers	Brain Anterior Caudate	brain
20	chr2:64070600-64073000	Active TSS	GM12878-XiMat	blood
21	chr2:64070600-64073400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:64070600-64073400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr2:64070600-64073800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr2:64070600-64074400	Weak transcription	A549	lung
25	chr2:64070600-64076600	Enhancers	Brain Substantia Nigra	brain
26	chr2:64070600-64082800	Weak transcription	Fetal Stomach	stomach
27	chr2:64070600-64083800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:64070800-64073000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:64070800-64073200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
30	chr2:64070800-64073400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:64070800-64073600	Flanking Active TSS	Fetal Heart	heart
32	chr2:64070800-64073800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:64070800-64075800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:64070800-64076000	Enhancers	Brain Hippocampus Middle	brain
35	chr2:64070800-64082600	Weak transcription	HUVEC	blood vessel
36	chr2:64071000-64073400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:64071000-64074200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:64071000-64076200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:64071200-64073000	Weak transcription	Osteobl	bone
40	chr2:64071200-64073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:64071200-64073200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
42	chr2:64071200-64073400	Enhancers	Brain Angular Gyrus	brain
43	chr2:64071200-64074000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr2:64071200-64074600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:64071200-64074600	Enhancers	HSMM	muscle
46	chr2:64071200-64075000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:64071200-64075000	Weak transcription	Brain Germinal Matrix	brain
48	chr2:64071200-64076000	Weak transcription	Fetal Kidney	kidney
49	chr2:64071200-64076200	Weak transcription	Fetal Lung	lung
50	chr2:64071200-64076400	Weak transcription	Fetal Brain Male	brain

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