Variant report

Variant	rs10942608
Chromosome Location	chr5:90082594-90082595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:90082585-90083064	K562	blood:	n/a	n/a
2	POLR2A	chr5:90082207-90083165	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90081164..90085224-chr5:90086154..90089719,5	K562	blood:

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10071548	1.00[ASN][1000 genomes]
rs11744148	1.00[ASN][1000 genomes]
rs12109698	1.00[LWK][hapmap]
rs17554631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17624740	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs2443086	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308293	1.00[ASN][1000 genomes]
rs57218688	1.00[ASN][1000 genomes]
rs62375135	1.00[ASN][1000 genomes]
rs62375138	1.00[ASN][1000 genomes]
rs6875416	1.00[ASN][1000 genomes]
rs72784606	1.00[ASN][1000 genomes]
rs73185169	1.00[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:25 , 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	chr5:90066400-90083800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:90069400-90089400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:90074800-90086800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:90075600-90084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:90075800-90086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:90076200-90086600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:90078400-90089800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:90079600-90089400	Weak transcription	Fetal Brain Male	brain
16	chr5:90080200-90083000	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:90080600-90082600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:90080600-90086800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:90081000-90083600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:90082000-90083600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:90082200-90089800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:90082200-90090000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr5:90082400-90082600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:90082400-90085400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:90082400-90087400	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links