Variant report

Variant	rs1992549
Chromosome Location	chr1:172224479-172224480
allele	C/T
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	chr1:172223524..172225386-chr1:172246377..172249330,2	MCF-7	breast:
2	chr1:172224104..172227089-chr1:172327866..172331463,5	MCF-7	breast:
3	chr1:172221315..172226024-chr1:172325981..172331432,5	MCF-7	breast:
4	chr1:172223489..172225833-chr1:172289738..172293302,4	MCF-7	breast:
5	chr1:172217494..172219854-chr1:172223387..172225787,2	MCF-7	breast:
6	chr1:172223818..172226357-chr1:172229730..172231454,2	MCF-7	breast:
7	chr1:172223432..172226037-chr1:172367106..172368941,2	MCF-7	breast:
8	chr1:172223330..172225504-chr1:172229542..172231885,2	MCF-7	breast:

No data

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10158839	0.84[CEU][hapmap]
rs10797969	0.84[CEU][hapmap]
rs11590165	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12038494	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041600	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12737669	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12740971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1992550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992551	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224567	0.84[CEU][hapmap]
rs2255690	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2586393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2586416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2757504	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41481754	0.84[CEU][hapmap]
rs4916245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520918	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6424841	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424865	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6694387	0.92[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9425287	0.84[CEU][hapmap]
rs9425560	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172208800-172227600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:172209800-172230800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:172216400-172229200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:172221200-172225000	Enhancers	NHDF-Ad	bronchial
5	chr1:172221200-172225400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:172223000-172225000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:172223000-172225200	Enhancers	Osteobl	bone
8	chr1:172223000-172225600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:172223200-172224600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:172223200-172225400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:172223400-172230600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:172223600-172225000	Enhancers	HSMMtube	muscle
13	chr1:172223600-172225200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:172223600-172225200	Enhancers	NHEK	skin
15	chr1:172223600-172225400	Enhancers	Hela-S3	cervix
16	chr1:172223600-172225400	Enhancers	HMEC	breast
17	chr1:172223600-172225400	Enhancers	HSMM	muscle
18	chr1:172223800-172224800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:172223800-172224800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:172223800-172224800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:172223800-172224800	Flanking Active TSS	A549	lung
22	chr1:172223800-172224800	Enhancers	NHLF	lung
23	chr1:172223800-172225200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:172224000-172224600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:172224000-172224600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:172224000-172225000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:172224200-172224600	Enhancers	Primary T cells from cord blood	blood
28	chr1:172224200-172224600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:172224200-172224600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr1:172224200-172224600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:172224200-172224600	Enhancers	Dnd41	blood
32	chr1:172224200-172224800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:172224200-172224800	Enhancers	GM12878-XiMat	blood
34	chr1:172224200-172225000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:172224200-172225000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:172224200-172225000	Active TSS	Aorta	Aorta
37	chr1:172224400-172224800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:172224400-172224800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr1:172224400-172224800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:172224400-172225000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:172224400-172225400	Flanking Active TSS	HUVEC	blood vessel
42	chr1:172224400-172225400	Flanking Active TSS	NH-A	brain

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