Variant report

Variant	rs11745840
Chromosome Location	chr5:126794420-126794421
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10491250	1.00[CEU][hapmap]
rs10519935	1.00[CEU][hapmap]
rs10519940	1.00[YRI][hapmap]
rs11241930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11743165	0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11743831	0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11743942	0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs11747639	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11750372	1.00[YRI][hapmap]
rs11750401	1.00[YRI][hapmap]
rs11950754	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11950816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12109001	1.00[CEU][hapmap]
rs1363386	1.00[CEU][hapmap]
rs1529468	1.00[CEU][hapmap]
rs1587628	0.88[EUR][1000 genomes]
rs1592960	0.88[EUR][1000 genomes]
rs17164854	1.00[CEU][hapmap]
rs17164922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17164923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17164929	1.00[YRI][hapmap]
rs17164938	0.85[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs17164951	1.00[CEU][hapmap]
rs17164957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17165013	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17165018	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17165019	1.00[CEU][hapmap]
rs17684644	1.00[CEU][hapmap]
rs17684655	1.00[CEU][hapmap]
rs17684679	1.00[CEU][hapmap]
rs17684691	1.00[CEU][hapmap]
rs17684740	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs17684775	1.00[CEU][hapmap]
rs17685202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17763126	1.00[CEU][hapmap]
rs17763172	1.00[CEU][hapmap]
rs17839692	1.00[YRI][hapmap]
rs1990954	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs1990955	1.00[CEU][hapmap]
rs2042942	1.00[CEU][hapmap]
rs2134252	0.88[EUR][1000 genomes]
rs2270931	1.00[YRI][hapmap]
rs2270933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851468	1.00[CEU][hapmap]
rs41298320	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861432	0.88[EUR][1000 genomes]
rs57626860	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6595773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865700	1.00[CEU][hapmap]
rs6866275	1.00[CEU][hapmap]
rs6873921	1.00[CEU][hapmap]
rs6874260	1.00[CEU][hapmap]
rs6877383	1.00[CEU][hapmap]
rs6883445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73331215	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7737871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929781	1.00[CEU][hapmap]
rs929782	1.00[CEU][hapmap]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126774600-126798800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:126778000-126795400	Weak transcription	Brain Angular Gyrus	brain
3	chr5:126781800-126794800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:126782600-126795200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:126783400-126795600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:126783800-126797200	Weak transcription	HSMM	muscle
7	chr5:126785200-126797000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:126785400-126794800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:126786000-126797600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:126788800-126797800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:126789400-126797000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:126789800-126797000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:126790200-126797200	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:126791400-126797200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:126792800-126795600	Strong transcription	HSMMtube	muscle
17	chr5:126793200-126798000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:126793400-126796800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:126793400-126797000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:126793400-126797000	Weak transcription	Brain Anterior Caudate	brain
21	chr5:126793400-126797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:126793400-126799600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:126793400-126805200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:126793800-126795400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:126794000-126797000	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links