Variant report

Variant	rs2438343
Chromosome Location	chr5:90161605-90161606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90153756..90156660-chr5:90161187..90163810,2	K562	blood:
2	chr5:90160869..90165602-chr5:90675521..90682094,8	K562	blood:
3	chr5:90158577..90166779-chr5:90674301..90681062,16	MCF-7	breast:
4	chr5:90159385..90163869-chr5:90675528..90680815,7	MCF-7	breast:
5	chr5:90161212..90166184-chr5:90674566..90680439,9	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10044202	0.82[ASN][1000 genomes]
rs10045071	0.84[CHB][hapmap]
rs10052015	0.92[CHB][hapmap]
rs10053303	0.92[CHB][hapmap]
rs10059629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10060641	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs10061193	0.83[ASN][1000 genomes]
rs10078496	0.92[CHB][hapmap]
rs10474336	0.83[CHB][hapmap]
rs10514339	0.97[CHD][hapmap]
rs10514340	0.84[CHB][hapmap]
rs12054681	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs12520956	0.91[CHB][hapmap]
rs12522395	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs13159353	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16869175	0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2247415	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2247419	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2247546	0.82[EUR][1000 genomes]
rs2247870	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2366935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2438338	0.93[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2438342	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438345	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438351	0.82[CHB][hapmap]
rs2438353	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2443068	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs2443089	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3098356	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916698	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs4916826	0.83[ASN][1000 genomes]
rs4916827	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4916828	0.82[ASN][1000 genomes]
rs4916829	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs57107124	0.86[ASN][1000 genomes]
rs6865577	0.90[ASN][1000 genomes]
rs6878896	0.92[CHB][hapmap]
rs7724016	0.92[CHB][hapmap]
rs881289	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2438343	GPR98	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90112000-90175800	Weak transcription	Fetal Brain Female	brain
2	chr5:90142600-90162400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:90148200-90171400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:90148400-90164800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:90151600-90162400	Weak transcription	K562	blood
6	chr5:90151800-90174000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:90151800-90174600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:90152000-90165000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:90158200-90162400	Weak transcription	Brain Anterior Caudate	brain
10	chr5:90159600-90164600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:90159800-90162200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:90159800-90162400	Weak transcription	Stomach Mucosa	stomach
13	chr5:90159800-90164800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:90160400-90162400	Enhancers	Liver	Liver
15	chr5:90160400-90164000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:90160600-90163200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:90160800-90163200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:90161200-90161800	Weak transcription	Fetal Brain Male	brain
19	chr5:90161600-90162400	Enhancers	Brain Germinal Matrix	brain
20	chr5:90161600-90162600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links