Variant report

Variant	rs1886831
Chromosome Location	chr1:62760400-62760401
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: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10889317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207949	0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs12037540	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044289	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12064402	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12082623	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12095092	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12095173	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1325742	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666483	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs2666501	0.86[EUR][1000 genomes]
rs2666502	0.88[EUR][1000 genomes]
rs2765265	0.83[CEU][hapmap]
rs2765267	0.83[CEU][hapmap]
rs3844053	0.81[TSI][hapmap]
rs3844054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850631	0.90[EUR][1000 genomes]
rs3895339	0.81[EUR][1000 genomes]
rs4915609	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4915811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915812	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4915813	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4915814	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4915815	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587965	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663943	0.91[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs7551135	0.89[EUR][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:38 , 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	chr1:62755600-62761000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62756400-62764800	Weak transcription	HepG2	liver
8	chr1:62759800-62760400	Enhancers	HMEC	breast
9	chr1:62759800-62760600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:62759800-62760600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:62759800-62761800	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
14	chr1:62760000-62760400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:62760000-62760600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:62760000-62760600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:62760000-62760600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:62760000-62760800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:62760000-62760800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
20	chr1:62760000-62761200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:62760000-62761200	Weak transcription	HSMMtube	muscle
22	chr1:62760000-62761600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:62760200-62760400	Enhancers	Placenta	Placenta
25	chr1:62760200-62760400	Enhancers	Fetal Thymus	thymus
26	chr1:62760200-62761000	Weak transcription	Fetal Stomach	stomach
27	chr1:62760200-62761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:62760200-62761200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:62760200-62761200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:62760200-62761600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:62760200-62761600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:62760400-62760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:62760400-62760800	Weak transcription	HMEC	breast
34	chr1:62760400-62761200	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:62760400-62761200	Weak transcription	Placenta	Placenta
36	chr1:62760400-62762000	Enhancers	Brain Angular Gyrus	brain
37	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
38	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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