Variant report

Variant	rs17097091
Chromosome Location	chr12:47056575-47056576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46972689..46974788-chr12:47053934..47056734,2	MCF-7	breast:
2	chr12:46763815..46766658-chr12:47056305..47059376,3	K562	blood:
3	chr12:46750763..46752796-chr12:47055390..47058156,2	MCF-7	breast:
4	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
5	chr12:46383988..46386138-chr12:47055082..47056612,2	MCF-7	breast:
6	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
7	chr12:46775360..46780494-chr12:47054865..47060216,9	MCF-7	breast:
8	chr12:46887516..46889882-chr12:47054053..47056770,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000258096	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11183519	0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs11183551	0.86[AMR][1000 genomes]
rs11183610	0.85[CHB][hapmap]
rs12301214	0.85[CHB][hapmap]
rs12301825	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs12307687	0.82[CHB][hapmap]
rs12311952	0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs12318944	0.82[AMR][1000 genomes]
rs12579010	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12579419	0.96[AMR][1000 genomes]
rs12579984	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12580176	0.94[AMR][1000 genomes]
rs12581743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12582056	0.80[YRI][hapmap]
rs1266371	0.84[AMR][1000 genomes]
rs17097079	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17097141	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17097246	0.85[CHB][hapmap]
rs1946174	0.85[AMR][1000 genomes]
rs1986154	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2160892	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2287470	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2408616	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2897979	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4351902	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768124	0.81[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs4768126	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768738	0.89[ASN][1000 genomes]
rs4768740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4768746	0.86[ASN][1000 genomes]
rs4768747	0.94[ASN][1000 genomes]
rs4768749	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768758	0.85[CHB][hapmap]
rs4768759	0.85[CHB][hapmap]
rs57616927	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58806862	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59408501	0.82[AMR][1000 genomes]
rs6582676	0.85[CHB][hapmap]
rs7132144	0.80[AMR][1000 genomes]
rs7133051	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7310614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7311414	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7315740	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73282105	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73282110	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7487359	0.85[CHB][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs7487705	0.84[YRI][hapmap]
rs7959179	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7971812	0.89[ASN][1000 genomes]
rs7976531	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7976785	0.80[AMR][1000 genomes]
rs7979449	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47046800-47057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:47053400-47058200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr12:47053400-47058600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:47053400-47062400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:47053800-47058800	Enhancers	Hela-S3	cervix
8	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:47054400-47057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:47054400-47059400	Weak transcription	Psoas Muscle	Psoas
12	chr12:47054600-47058200	Enhancers	NHEK	skin
13	chr12:47054800-47058200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:47055000-47058600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:47055200-47057000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:47055200-47057000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:47055200-47058400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:47055200-47058600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:47055200-47058600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:47055400-47057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:47055400-47058200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:47055400-47058600	Weak transcription	Primary B cells from cord blood	blood
23	chr12:47055400-47059600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:47055600-47058200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:47055600-47058200	Weak transcription	K562	blood
26	chr12:47055600-47058400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:47055600-47058600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:47055600-47058600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:47055600-47058600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:47055600-47059000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:47055600-47059400	Weak transcription	Fetal Kidney	kidney
32	chr12:47055800-47056800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:47055800-47057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:47055800-47057000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:47055800-47057000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:47055800-47057000	Weak transcription	A549	lung
37	chr12:47055800-47057000	Weak transcription	HSMM	muscle
38	chr12:47055800-47057000	Weak transcription	HSMMtube	muscle
39	chr12:47055800-47058000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:47055800-47058000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:47056000-47057000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:47056000-47057000	Weak transcription	HepG2	liver
43	chr12:47056000-47057000	Weak transcription	NHLF	lung
44	chr12:47056000-47057000	Weak transcription	Osteobl	bone
45	chr12:47056000-47058000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:47056000-47058000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:47056000-47058000	Weak transcription	NH-A	brain
48	chr12:47056000-47058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:47056000-47058200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:47056000-47058400	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links