Variant report

Variant	rs13254942
Chromosome Location	chr8:10257678-10257679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11249992	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11249995	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11249996	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249999	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11250001	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11250002	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11779205	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11785061	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11989640	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12156350	0.88[CEU][hapmap]
rs12541491	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12543645	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12547997	0.90[ASW][hapmap];0.84[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12548025	0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12550717	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13264580	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17151903	0.89[CHD][hapmap]
rs17767186	0.83[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs1986972	0.96[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2001337	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001338	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3088186	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs34155841	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34381075	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34487437	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060302	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35406700	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35472251	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35840352	0.90[EUR][1000 genomes]
rs4240645	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4292737	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4316191	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4841329	0.87[CEU][hapmap]
rs6985267	0.84[CHD][hapmap]
rs6999466	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7460436	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7840461	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs9650650	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9657538	0.83[ASN][1000 genomes]
rs9657539	0.81[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv465460	chr8:10241411-10290566	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv610265	chr8:10241411-10290566	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv610266	chr8:10250758-10294330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv1019701	chr8:10254709-10279269	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13254942	CLDN23	cis	multi-tissue	Pritchard
rs13254942	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs13254942	FLJ10661	cis	parietal	SCAN
rs13254942	RP1L1	cis	cerebellum	SCAN
rs13254942	FLJ10661	cis	cerebellum	SCAN
rs13254942	PPP1R3B	cis	cerebellum	SCAN
rs13254942	DEFB136	cis	parietal	SCAN
rs13254942	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs13254942	MFHAS1	cis	cerebellum	SCAN
rs13254942	C8orf13	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10249000-10258200	Enhancers	Fetal Muscle Leg	muscle
3	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr8:10252000-10258200	Enhancers	Fetal Muscle Trunk	muscle
5	chr8:10253800-10257800	Weak transcription	Spleen	Spleen
6	chr8:10254200-10261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr8:10255200-10267800	Weak transcription	Primary T cells from cord blood	blood
8	chr8:10256000-10258000	Enhancers	Fetal Brain Male	brain
9	chr8:10256000-10267600	Weak transcription	Brain Angular Gyrus	brain
10	chr8:10256400-10260600	Weak transcription	Fetal Brain Female	brain
11	chr8:10256800-10258200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:10256800-10258400	Weak transcription	Psoas Muscle	Psoas
13	chr8:10256800-10266400	Weak transcription	Fetal Heart	heart
14	chr8:10257000-10257800	Weak transcription	Brain Hippocampus Middle	brain
15	chr8:10257000-10267600	Weak transcription	Right Ventricle	heart
16	chr8:10257000-10274400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr8:10257200-10257800	Weak transcription	Liver	Liver
18	chr8:10257400-10258000	Weak transcription	Pancreas	Pancrea
19	chr8:10257600-10259600	Weak transcription	HSMMtube	muscle
20	chr8:10257600-10267000	Weak transcription	Right Atrium	heart

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