Variant report

Variant	rs12078087
Chromosome Location	chr1:62761126-62761127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62759279..62761889-chr1:62763662..62766108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201153	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207957	0.89[ASN][1000 genomes]
rs12058486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12065844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12079207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12082238	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12085325	0.98[ASN][1000 genomes]
rs12718429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12724349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12760895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296518	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2477872	0.97[ASN][1000 genomes]
rs2666487	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2666488	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2666503	0.82[AMR][1000 genomes]
rs2666506	0.82[AMR][1000 genomes]
rs2666508	0.82[AMR][1000 genomes]
rs2765251	0.84[AMR][1000 genomes]
rs2765258	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2765261	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2765263	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34752481	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516290	0.82[AMR][1000 genomes]
rs7520614	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs765691	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs765692	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs912894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs912895	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs912896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62753200-62761600	Weak transcription	Pancreas	Pancrea
2	chr1:62753200-62761600	Weak transcription	Right Atrium	heart
3	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
5	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:62756400-62764800	Weak transcription	HepG2	liver
7	chr1:62759800-62761800	Enhancers	Fetal Muscle Trunk	muscle
8	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
10	chr1:62760000-62761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:62760000-62761200	Weak transcription	HSMMtube	muscle
12	chr1:62760000-62761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:62760200-62761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:62760200-62761200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:62760200-62761200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:62760200-62761600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:62760200-62761600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:62760400-62761200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:62760400-62761200	Weak transcription	Placenta	Placenta
21	chr1:62760400-62762000	Enhancers	Brain Angular Gyrus	brain
22	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
23	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:62760600-62761400	Weak transcription	Fetal Thymus	thymus
25	chr1:62760600-62761600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:62760800-62761200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:62760800-62761200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:62760800-62761600	Enhancers	HMEC	breast
29	chr1:62760800-62761800	Enhancers	Brain Cingulate Gyrus	brain
30	chr1:62760800-62762400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:62761000-62761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:62761000-62761800	Enhancers	HSMM	muscle
33	chr1:62761000-62762000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:62761000-62762000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:62761000-62762200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr1:62761000-62762200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:62761000-62762200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:62761000-62762400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:62761000-62762400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:62761000-62762400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:62761000-62763200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links