Variant report

Variant	rs8141404
Chromosome Location	chr22:30474216-30474217
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	RELA	chr22:30474149-30475490	GM12891	blood:	n/a	chr22:30475180-30475189 chr22:30475180-30475189

Variant related genes	Relation type
HORMAD2	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10048885	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11090598	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12167333	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12168499	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12171061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12171250	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12171263	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17648725	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1807509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs193473	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193481	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978083	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2017677	0.87[EUR][1000 genomes]
rs2051764	0.87[EUR][1000 genomes]
rs2412960	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412963	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs28257	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36580	0.83[AMR][1000 genomes]
rs36590	0.83[AMR][1000 genomes]
rs36591	0.83[AMR][1000 genomes]
rs36594	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36596	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36598	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36600	0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36601	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36604	0.95[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36605	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36606	0.82[AMR][1000 genomes]
rs36607	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3788423	0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3887275	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs39712	0.83[AMR][1000 genomes]
rs41162	0.84[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs41164	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs41166	0.85[EUR][1000 genomes]
rs41172	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs41174	0.91[CEU][hapmap]
rs41175	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41177	0.80[CEU][hapmap]
rs41179	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4239932	0.95[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4239933	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4337577	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4823063	0.95[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4823070	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5752986	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5752988	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5752993	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763630	0.82[EUR][1000 genomes]
rs5763634	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763644	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5763674	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763675	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763680	0.87[EUR][1000 genomes]
rs5763689	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs715523	0.86[EUR][1000 genomes]
rs718772	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737904	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs737909	0.95[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs737912	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7510705	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8135823	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8136147	0.81[AMR][1000 genomes]
rs8138286	0.89[EUR][1000 genomes]
rs8141680	1.00[YRI][hapmap]
rs8141765	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9614162	0.82[YRI][hapmap]
rs9620943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620953	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9625919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9625921	0.80[CEU][hapmap]
rs9625926	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625931	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9625933	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9625935	0.86[EUR][1000 genomes]

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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8141404	NEFH	cis	cerebellum	SCAN
rs8141404	CRYBB3	cis	parietal	SCAN
rs8141404	MTMR3	cis	multi-tissue	Pritchard
rs8141404	TTC28	cis	cerebellum	SCAN
rs8141404	KIAA1671	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30461600-30474600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr22:30472000-30474800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr22:30473000-30474400	Enhancers	Fetal Intestine Small	intestine
4	chr22:30473000-30474400	Enhancers	HepG2	liver
5	chr22:30473000-30474600	Enhancers	GM12878-XiMat	blood
6	chr22:30473400-30476000	Enhancers	Liver	Liver
7	chr22:30473400-30476400	Weak transcription	Fetal Lung	lung
8	chr22:30473800-30475400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr22:30474000-30474400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr22:30474000-30475400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr22:30474000-30475400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr22:30474000-30475400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr22:30474000-30475400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr22:30474000-30475600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr22:30474200-30474400	Enhancers	Fetal Brain Male	brain
16	chr22:30474200-30475000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr22:30474200-30475000	Enhancers	Fetal Thymus	thymus
18	chr22:30474200-30475400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr22:30474200-30476000	Weak transcription	Lung	lung
20	chr22:30474200-30476200	Weak transcription	Fetal Intestine Large	intestine

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