Variant report

Variant	rs10054610
Chromosome Location	chr5:111520813-111520814
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111514597..111516763-chr5:111520415..111522514,2	K562	blood:
2	chr5:111501005..111502914-chr5:111519485..111522165,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10043186	0.89[AMR][1000 genomes]
rs10054560	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10069011	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1078128	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241153	0.96[CEU][hapmap];0.89[AMR][1000 genomes]
rs12655385	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13165611	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1560053	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560054	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560055	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1560057	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1560058	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1863960	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1981954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2416277	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4957632	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4957634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4957636	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4958002	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958003	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958004	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958007	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4958008	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4958009	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4958010	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4958012	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4958013	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4958014	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4958015	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59537089	0.81[AMR][1000 genomes]
rs6594569	0.85[AMR][1000 genomes]
rs6594571	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594574	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6863063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6876893	0.95[CEU][hapmap];0.92[AMR][1000 genomes]
rs6884589	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7704087	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs7706160	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7709484	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7710973	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7711158	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7716309	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7717363	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7719346	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs890757	0.87[CEU][hapmap]
rs890758	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111497600-111538600	Weak transcription	Small Intestine	intestine
2	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
3	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
4	chr5:111502800-111546000	Weak transcription	Ovary	ovary
5	chr5:111503600-111527800	Weak transcription	Psoas Muscle	Psoas
6	chr5:111503600-111537400	Weak transcription	Lung	lung
7	chr5:111504800-111541400	Weak transcription	Right Ventricle	heart
8	chr5:111504800-111557800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:111504800-111586400	Weak transcription	Gastric	stomach
10	chr5:111505000-111521000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:111505000-111537400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:111505600-111521000	Weak transcription	Placenta	Placenta
13	chr5:111505600-111541800	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:111510800-111540000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:111510800-111547400	Weak transcription	HUVEC	blood vessel
16	chr5:111519000-111546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:111519200-111532600	Weak transcription	Fetal Kidney	kidney
18	chr5:111519200-111537400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:111519200-111553800	Weak transcription	Pancreas	Pancrea
20	chr5:111519400-111522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:111519400-111524800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:111519400-111529200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:111519400-111530600	Weak transcription	Left Ventricle	heart
24	chr5:111519400-111531800	Weak transcription	Fetal Heart	heart
25	chr5:111519600-111521600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:111519600-111521600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:111519600-111530400	Weak transcription	Adipose Nuclei	Adipose
28	chr5:111519800-111521400	Weak transcription	HMEC	breast
29	chr5:111519800-111553600	Weak transcription	Esophagus	oesophagus
30	chr5:111520400-111529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:111520600-111527800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links