Variant report

Variant	rs11956622
Chromosome Location	chr5:90086216-90086217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90077865..90080476-chr5:90084014..90086656,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10514337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10514338	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs11950742	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs11959536	0.81[YRI][hapmap]
rs11959781	0.85[AFR][1000 genomes]
rs12655163	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12655900	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12657829	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16869112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16869117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16869133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16869139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16869140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16869151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16869154	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs16869163	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1983366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2203823	0.89[CHB][hapmap]
rs2366932	0.96[ASN][1000 genomes]
rs2438339	0.89[CHB][hapmap]
rs2438352	0.81[JPT][hapmap]
rs2438361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2438366	0.92[ASN][1000 genomes]
rs2438375	0.88[ASN][1000 genomes]
rs2438377	0.86[ASN][1000 genomes]
rs2438379	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2438380	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2443076	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs2443084	0.88[ASN][1000 genomes]
rs28757668	0.80[AFR][1000 genomes]
rs3107223	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs3763073	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6860302	0.85[AFR][1000 genomes]
rs6880683	0.85[AFR][1000 genomes]
rs7717221	0.81[AFR][1000 genomes]
rs7729495	0.85[AFR][1000 genomes]
rs7732226	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7735712	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs879571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
4	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1031718	chr5:89999033-90099868	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90043600-90086800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:90048400-90089200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:90051800-90105000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:90061200-90090800	Weak transcription	Brain Anterior Caudate	brain
5	chr5:90065000-90087000	Weak transcription	Fetal Brain Female	brain
6	chr5:90066200-90087000	Weak transcription	Brain Germinal Matrix	brain
7	chr5:90066200-90089800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:90069400-90089400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:90074800-90086800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:90076200-90086600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:90078400-90089800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:90079600-90089400	Weak transcription	Fetal Brain Male	brain
13	chr5:90080600-90086800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:90082200-90089800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:90082200-90090000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:90082400-90087400	Strong transcription	K562	blood
17	chr5:90082600-90090200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:90082800-90090600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:90083000-90086800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:90083600-90088600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:90083600-90089200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:90083600-90090400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:90085000-90086600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:90085200-90090400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:90085200-90090400	Weak transcription	Pancreas	Pancrea
26	chr5:90086200-90090200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:90086200-90090200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:90086200-90092200	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links