Variant report

Variant	rs6426492
Chromosome Location	chr1:228322826-228322827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228320957..228324264-chr1:228357884..228361663,3	MCF-7	breast:
2	chr1:228321585..228323850-chr1:228673376..228675624,2	K562	blood:
3	chr1:228319215..228325156-chr1:228326279..228328957,6	K562	blood:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1059778	0.81[CEU][hapmap]
rs10753445	0.81[CEU][hapmap]
rs10799469	0.81[EUR][1000 genomes]
rs10916277	0.81[EUR][1000 genomes]
rs11584385	0.81[CEU][hapmap]
rs12084338	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes]
rs12097591	0.82[EUR][1000 genomes]
rs12130630	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12134624	0.88[CEU][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12745416	0.81[CEU][hapmap]
rs1411910	0.81[CEU][hapmap]
rs1557026	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs1620111	0.81[CEU][hapmap]
rs1629294	0.81[CEU][hapmap]
rs1757132	0.81[CEU][hapmap]
rs1757133	0.81[CEU][hapmap]
rs1757139	0.81[CEU][hapmap]
rs1757149	0.81[CEU][hapmap]
rs1757150	0.81[CEU][hapmap]
rs1757152	0.80[CEU][hapmap]
rs1757156	0.81[CEU][hapmap]
rs17623766	0.82[EUR][1000 genomes]
rs17640616	0.96[CEU][hapmap]
rs1771459	0.81[CEU][hapmap]
rs1771460	0.81[CEU][hapmap]
rs1771474	0.81[CEU][hapmap]
rs1771476	0.81[CEU][hapmap]
rs1771479	0.80[CEU][hapmap]
rs1771482	0.81[CEU][hapmap]
rs1771483	0.81[CEU][hapmap]
rs1771484	0.87[CEU][hapmap]
rs1771485	0.80[CEU][hapmap]
rs2066237	0.80[CEU][hapmap]
rs2298014	0.87[EUR][1000 genomes]
rs2313600	0.82[EUR][1000 genomes]
rs2313601	0.80[CEU][hapmap]
rs2313602	0.81[CEU][hapmap]
rs2776855	0.81[CEU][hapmap]
rs2776856	0.81[CEU][hapmap]
rs2872538	0.81[CEU][hapmap]
rs3845621	0.84[YRI][hapmap]
rs4653907	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653917	0.96[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4653919	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4653920	0.86[EUR][1000 genomes]
rs4653921	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs55873533	0.87[EUR][1000 genomes]
rs6657968	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6673893	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs6682260	0.96[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6704220	0.87[LWK][hapmap];0.90[YRI][hapmap]
rs708123	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap]
rs72757811	0.89[EUR][1000 genomes]
rs72757812	0.87[EUR][1000 genomes]
rs72757824	0.83[EUR][1000 genomes]
rs72757827	0.83[EUR][1000 genomes]
rs7512209	0.81[CEU][hapmap]
rs752107	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7523917	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs7532924	0.80[CEU][hapmap]
rs7537636	0.81[CEU][hapmap]
rs7539762	0.96[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs766972	0.94[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs822725	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs822739	0.81[ASN][1000 genomes]
rs822740	0.81[ASN][1000 genomes]
rs849749	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[ASN][1000 genomes]
rs947087	0.81[CEU][hapmap]
rs9728319	0.92[YRI][hapmap]

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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6426492	OBSCN	cis	Esophagus Mucosa	GTEx
rs6426492	ITPKB	cis	cerebellum	SCAN
rs6426492	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs6426492	WDR26	cis	cerebellum	SCAN
rs6426492	MRPL55	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228318800-228324000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:228318800-228327000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:228318800-228327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:228319000-228323400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:228319000-228323600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:228319000-228323600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:228319000-228323600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:228319000-228325000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:228319200-228324400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:228322600-228323600	Enhancers	K562	blood

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