Variant report

Variant	rs9620988
Chromosome Location	chr22:30847934-30847935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30847099..30849207-chr22:30861572..30863598,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1047917	0.88[ASN][1000 genomes]
rs1057995	0.88[ASN][1000 genomes]
rs11089451	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465222	0.97[ASN][1000 genomes]
rs1465224	0.97[ASN][1000 genomes]
rs2015166	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074650	0.88[ASN][1000 genomes]
rs2240345	0.88[ASN][1000 genomes]
rs2269963	0.85[ASN][1000 genomes]
rs2412986	0.88[ASN][1000 genomes]
rs2412987	0.88[ASN][1000 genomes]
rs2412988	0.88[ASN][1000 genomes]
rs2899150	0.95[ASN][1000 genomes]
rs3804078	0.87[ASN][1000 genomes]
rs4820848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820850	0.88[ASN][1000 genomes]
rs4820851	0.88[ASN][1000 genomes]
rs4820854	0.85[ASN][1000 genomes]
rs4820856	0.85[ASN][1000 genomes]
rs4820857	0.85[ASN][1000 genomes]
rs4820858	0.85[ASN][1000 genomes]
rs5749095	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749103	0.88[ASN][1000 genomes]
rs5749104	0.88[ASN][1000 genomes]
rs5749105	0.87[ASN][1000 genomes]
rs5753143	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753146	0.97[ASN][1000 genomes]
rs5753150	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5753151	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753152	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753156	0.85[ASN][1000 genomes]
rs5753157	0.88[ASN][1000 genomes]
rs5753160	0.88[ASN][1000 genomes]
rs5753161	0.85[ASN][1000 genomes]
rs5753162	0.85[ASN][1000 genomes]
rs5997650	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997653	0.85[ASN][1000 genomes]
rs5997654	0.85[ASN][1000 genomes]
rs5997655	0.85[ASN][1000 genomes]
rs5997656	0.85[ASN][1000 genomes]
rs757662	0.88[ASN][1000 genomes]
rs757663	0.85[ASN][1000 genomes]
rs8135169	0.85[ASN][1000 genomes]
rs8141805	0.88[ASN][1000 genomes]
rs9306260	0.85[ASN][1000 genomes]
rs9306261	0.85[ASN][1000 genomes]
rs9608922	0.82[AMR][1000 genomes]
rs9620998	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv459870	chr22:30836313-30868418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv588886	chr22:30836313-30868418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv966047	chr22:30844219-30851600	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9620988	SEC14L3	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30832000-30850000	Weak transcription	Right Atrium	heart
2	chr22:30832200-30852400	Weak transcription	Spleen	Spleen
3	chr22:30841800-30850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30846600-30848000	Enhancers	Fetal Intestine Large	intestine
5	chr22:30846600-30848200	Enhancers	Fetal Intestine Small	intestine
6	chr22:30846800-30848400	Enhancers	K562	blood
7	chr22:30847000-30849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:30847400-30848400	Weak transcription	Ovary	ovary
9	chr22:30847400-30854200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links