Variant report

Variant	rs9404043
Chromosome Location	chr6:149871948-149871949
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149871886..149874097-chr6:149885143..149886769,2	K562	blood:
2	chr6:149863453..149865159-chr6:149871919..149873635,2	MCF-7	breast:
3	chr6:149867140..149870243-chr6:149871733..149875338,4	K562	blood:
4	chr6:149867616..149870939-chr6:149871869..149874577,3	K562	blood:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10485097	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1125107	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12524946	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12663698	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665533	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474640	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17732745	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2105200	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2341550	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341551	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2341768	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28580659	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880075	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3813675	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4869797	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4897128	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4897130	0.81[ASN][1000 genomes]
rs4897131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897132	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897133	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4897137	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897138	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897139	0.87[EUR][1000 genomes]
rs60404985	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62439778	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62442787	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62442788	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442789	0.86[ASN][1000 genomes]
rs62442790	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62442792	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62442793	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62442795	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62442798	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6570968	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6911016	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6929614	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs761617	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7753560	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7774559	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7774597	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs909792	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9322184	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9322185	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9373594	0.87[EUR][1000 genomes]
rs9373595	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373596	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377220	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377221	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377223	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9377224	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390684	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9390687	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390688	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9390689	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399689	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399690	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404042	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9404044	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9406344	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9498368	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9689569	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9800648	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv966665	chr6:149862756-149895103	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9404043	RP11-350J20.5	cis	Thyroid	GTEx
rs9404043	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9404043	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9404043	GINM1	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149868000-149873000	Weak transcription	Gastric	stomach
2	chr6:149868000-149873400	Weak transcription	Fetal Heart	heart
3	chr6:149871200-149872400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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