Variant report

Variant	rs1645412
Chromosome Location	chr5:89407917-89407918
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89406847..89409884-chr5:89414487..89417223,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10044667	0.87[EUR][1000 genomes]
rs10805864	0.81[EUR][1000 genomes]
rs10942581	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11949266	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11958908	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11958926	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12517492	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12519494	0.81[EUR][1000 genomes]
rs150133	0.89[ASN][1000 genomes]
rs154193	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1560208	0.81[EUR][1000 genomes]
rs157305	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157306	0.82[EUR][1000 genomes]
rs157307	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157308	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157311	0.82[EUR][1000 genomes]
rs157558	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs157559	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs157560	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs157564	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1596431	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs166820	0.82[EUR][1000 genomes]
rs1698137	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1698138	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1698139	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175965	0.92[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs176107	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2652732	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs280671	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs30713	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60448814	0.86[EUR][1000 genomes]
rs662339	0.92[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs6862722	0.87[EUR][1000 genomes]
rs6871792	0.81[EUR][1000 genomes]
rs690558	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs702845	0.92[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs818944	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs818945	0.82[EUR][1000 genomes]
rs818946	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs818947	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs818948	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs889293	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs924627	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs924628	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293534	0.82[EUR][1000 genomes]

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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89407200-89408000	Enhancers	HSMM	muscle
2	chr5:89407400-89408000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:89407400-89408000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:89407400-89408000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr5:89407400-89408000	Active TSS	Psoas Muscle	Psoas
6	chr5:89407400-89408000	Active TSS	Osteobl	bone
7	chr5:89407400-89408800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:89407600-89408000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:89407600-89408000	Active TSS	Brain Angular Gyrus	brain
10	chr5:89407600-89408000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr5:89407600-89408000	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr5:89407600-89408200	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr5:89407600-89408400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:89407600-89408600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr5:89407600-89408600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:89407800-89408000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:89407800-89408000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:89407800-89408000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:89407800-89408200	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links