Variant report

Variant	rs229963
Chromosome Location	chr5:56993290-56993291
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	chr5:56991984..56994307-chr5:57002292..57003964,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10057570	0.93[AFR][1000 genomes]
rs10057880	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10072292	1.00[YRI][hapmap]
rs10077005	1.00[AFR][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10487614	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12520986	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13185580	1.00[AFR][1000 genomes]
rs1347071	1.00[YRI][hapmap]
rs170740	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs170741	0.93[AFR][1000 genomes]
rs1821210	1.00[YRI][hapmap]
rs183477	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1861052	0.81[AFR][1000 genomes]
rs1861059	1.00[YRI][hapmap]
rs2017201	1.00[AFR][1000 genomes]
rs2041678	1.00[AFR][1000 genomes]
rs2161500	0.81[AFR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes]
rs2191446	1.00[AFR][1000 genomes]
rs2191448	1.00[AFR][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs229960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229961	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs229965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230846	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs230853	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs230860	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs230861	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2408849	1.00[AFR][1000 genomes]
rs2408850	0.86[AFR][1000 genomes]
rs2408854	1.00[YRI][hapmap]
rs2568537	1.00[YRI][hapmap]
rs2898028	1.00[AFR][1000 genomes]
rs4235474	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4403130	1.00[YRI][hapmap]
rs4458541	1.00[YRI][hapmap]
rs4508990	0.86[AFR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes]
rs4699913	1.00[YRI][hapmap]
rs4700214	1.00[AFR][1000 genomes]
rs4700233	1.00[YRI][hapmap]
rs6450430	0.82[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes]
rs6866242	0.86[AFR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7726732	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7732108	1.00[AFR][1000 genomes]
rs7737409	0.86[AFR][1000 genomes]
rs854036	1.00[YRI][hapmap]
rs917655	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs986101	1.00[AFR][1000 genomes]
rs991727	1.00[AFR][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56987400-56994800	Weak transcription	Right Ventricle	heart
2	chr5:56988200-56993400	Enhancers	Brain Angular Gyrus	brain
3	chr5:56988600-56995400	Enhancers	Adipose Nuclei	Adipose
4	chr5:56989400-56996000	Enhancers	Fetal Heart	heart
5	chr5:56989600-56993400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:56989600-56994000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:56989600-56994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:56989600-56996400	Weak transcription	Psoas Muscle	Psoas
9	chr5:56989800-56993600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:56989800-56993600	Weak transcription	HSMM	muscle
11	chr5:56990000-56993600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:56990000-56995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:56990200-57005600	Weak transcription	NH-A	brain
14	chr5:56990400-56996200	Enhancers	HMEC	breast
15	chr5:56990600-56993800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:56990600-56995000	Enhancers	Ovary	ovary
17	chr5:56990600-56996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:56991200-56993800	Enhancers	Fetal Muscle Leg	muscle
19	chr5:56991400-56993600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:56991400-56995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:56991400-56996000	Enhancers	NHEK	skin
22	chr5:56991600-56993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:56991600-56994000	Enhancers	Stomach Smooth Muscle	stomach
24	chr5:56991600-56994600	Weak transcription	Aorta	Aorta
25	chr5:56991800-56993400	Enhancers	Rectal Smooth Muscle	rectum
26	chr5:56992000-56993400	Enhancers	Liver	Liver
27	chr5:56992000-56993600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:56992000-56993800	Enhancers	Fetal Stomach	stomach
29	chr5:56992000-56994000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:56992000-56995600	Enhancers	HUVEC	blood vessel
31	chr5:56992200-56994800	Weak transcription	Right Atrium	heart
32	chr5:56992200-56996800	Enhancers	Fetal Lung	lung
33	chr5:56992400-56993600	Weak transcription	A549	lung
34	chr5:56992400-56993800	Enhancers	K562	blood
35	chr5:56992400-56995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:56992400-56995400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:56992400-56995400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:56992400-57004400	Weak transcription	Left Ventricle	heart
39	chr5:56992800-56993400	Enhancers	Colon Smooth Muscle	Colon
40	chr5:56992800-56994200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:56992800-56995000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:56993000-56993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:56993000-56993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:56993000-56994000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:56993000-56994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:56993000-56994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:56993000-56994400	Weak transcription	NHLF	lung
48	chr5:56993000-56994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:56993000-56994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:56993200-56994600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links