Variant report

Variant	rs238
Chromosome Location	chr9:98786276-98786277
allele	A/G
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	MAFK	chr9:98786187-98786422	HepG2	liver:	n/a	chr9:98786286-98786297 chr9:98786286-98786297

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98781352..98784533-chr9:98785992..98788272,3	MCF-7	breast:

Variant related genes	Relation type
LINC00092	TF binding region
ENSG00000225194	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10481647	0.89[CEU][hapmap]
rs10739632	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs10739787	0.87[JPT][hapmap]
rs10760675	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs10760692	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12004422	0.89[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs1627425	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2296857	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3930253	0.96[CEU][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743458	0.88[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs583716	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs585223	0.82[EUR][1000 genomes]
rs601916	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs615866	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs617884	0.80[EUR][1000 genomes]
rs626264	0.96[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs631273	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs636456	0.96[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs640281	0.85[EUR][1000 genomes]
rs643815	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6479036	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs676453	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678244	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs680468	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs680754	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs686604	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs689627	0.96[CEU][hapmap]
rs689749	0.92[CEU][hapmap]
rs689820	0.96[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs689871	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs689979	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs689980	0.83[AMR][1000 genomes]
rs690152	0.85[EUR][1000 genomes]
rs690222	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs690304	0.92[CEU][hapmap]
rs690335	0.81[EUR][1000 genomes]
rs690420	0.82[EUR][1000 genomes]
rs690455	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690484	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs690575	0.88[AMR][1000 genomes]
rs7024710	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7868559	0.82[EUR][1000 genomes]
rs7874897	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs913408	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9409322	0.82[GIH][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs238	LINC00476	cis	Nerve Tibial	GTEx
rs238	LINC00476	cis	Adipose Subcutaneous	GTEx
rs238	C9orf130	cis	cerebellum	SCAN
rs238	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs238	C9orf130	cis	parietal	SCAN
rs238	LINC00476	cis	lung	GTEx
rs238	C9orf102	cis	cerebellum	SCAN
rs238	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs238	LINC00476	cis	Artery Aorta	GTEx
rs238	LINC00476	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98784400-98788800	Weak transcription	Gastric	stomach
2	chr9:98785000-98788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:98785200-98786400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:98785200-98786600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:98785200-98788400	Weak transcription	Right Ventricle	heart
6	chr9:98785400-98786600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:98785400-98788800	Weak transcription	Brain Angular Gyrus	brain
8	chr9:98785400-98788800	Weak transcription	Ovary	ovary
9	chr9:98785400-98788800	Weak transcription	Right Atrium	heart
10	chr9:98785400-98789000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:98785400-98789000	Weak transcription	Spleen	Spleen
12	chr9:98785600-98786400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:98785600-98786400	Weak transcription	K562	blood
14	chr9:98785600-98786600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:98785600-98789000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:98785600-98789000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:98786000-98788800	Weak transcription	Fetal Lung	lung
18	chr9:98786200-98788800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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