Variant report

Variant	rs826881
Chromosome Location	chr12:39079033-39079034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39078731..39079461-chr2:68493058..68493608,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10400455	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10506128	1.00[GIH][hapmap];0.83[JPT][hapmap]
rs10783318	1.00[CEU][hapmap]
rs10875959	0.83[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs10875962	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs10875963	0.84[ASW][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs10875966	1.00[CEU][hapmap]
rs1095575	0.83[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs11169068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169137	0.91[ASN][1000 genomes]
rs11169142	0.81[AFR][1000 genomes]
rs12305675	1.00[GIH][hapmap]
rs12580077	0.83[JPT][hapmap]
rs12581365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1352122	0.83[JPT][hapmap]
rs1352123	0.83[JPT][hapmap]
rs1386017	1.00[CEU][hapmap]
rs1403523	0.82[JPT][hapmap]
rs1486345	0.82[JPT][hapmap]
rs1486346	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1684395	0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1684405	0.81[YRI][hapmap]
rs1684411	1.00[JPT][hapmap]
rs1684415	0.89[JPT][hapmap]
rs1684416	0.83[JPT][hapmap]
rs17126696	0.82[JPT][hapmap]
rs1719848	0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1719852	0.83[JPT][hapmap]
rs1719854	0.83[JPT][hapmap]
rs1719855	0.82[JPT][hapmap]
rs1719858	0.81[JPT][hapmap]
rs1872638	0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs2062759	1.00[CEU][hapmap]
rs2069211	0.83[JPT][hapmap]
rs2101370	0.84[ASW][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2221305	0.90[ASN][1000 genomes]
rs4238079	0.81[AFR][1000 genomes]
rs4300424	0.84[ASN][1000 genomes]
rs4767968	0.83[AFR][1000 genomes]
rs7309754	1.00[CEU][hapmap]
rs7957523	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs7971922	1.00[CEU][hapmap]
rs826838	0.83[JPT][hapmap];0.88[LWK][hapmap];0.88[YRI][hapmap]
rs826870	0.83[JPT][hapmap]
rs826876	0.83[JPT][hapmap]
rs826879	0.82[JPT][hapmap];0.81[AFR][1000 genomes]
rs826886	0.83[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs844116	1.00[CEU][hapmap]
rs923200	0.81[AFR][1000 genomes]
rs9645814	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs980571	0.83[JPT][hapmap]
rs980572	0.83[JPT][hapmap]
rs9943717	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers 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
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv3333662	chr12:39075385-39079683	ZNF genes & repeats Strong transcription Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
3	chr12:39051600-39080400	Weak transcription	Lung	lung
4	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:39055800-39100800	Weak transcription	NHEK	skin
6	chr12:39056000-39080200	Weak transcription	Ovary	ovary
7	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
10	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:39061200-39080400	Weak transcription	A549	lung
14	chr12:39061600-39080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:39063800-39080400	Weak transcription	Fetal Intestine Large	intestine
16	chr12:39063800-39082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
18	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:39069000-39080400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:39069800-39083000	Weak transcription	Left Ventricle	heart
22	chr12:39071600-39079200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
24	chr12:39075200-39080000	Weak transcription	Fetal Intestine Small	intestine
25	chr12:39075400-39080400	Strong transcription	Liver	Liver
26	chr12:39075800-39081200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:39077000-39079800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:39077800-39080800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:39078000-39079200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:39078200-39080400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:39078400-39079400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:39078400-39079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:39078400-39080200	Strong transcription	Adipose Nuclei	Adipose
34	chr12:39078600-39079400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:39079000-39079400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr12:39079000-39080400	Weak transcription	Brain Angular Gyrus	brain
37	chr12:39079000-39080600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr12:39079000-39080600	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links