Variant report

Variant	rs56226314
Chromosome Location	chr12:40919119-40919120
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	SPI1	chr12:40918937-40919169	GM12878	blood:	n/a	n/a
2	SPI1	chr12:40918749-40919364	HL-60	blood:	n/a	n/a
3	SPI1	chr12:40918940-40919283	HL-60	blood:	n/a	n/a
4	GABPA	chr12:40918691-40919382	HL-60	blood:	n/a	n/a
5	SPI1	chr12:40918973-40919155	GM12891	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN1-1	chr12:40918318-40919423	XLOC_009713
2	lnc-CNTN1-1	chr12:40918318-40919423	NONHSAT027733

Variant related genes	Relation type
MUC19	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1122621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564109	1.00[ASN][1000 genomes]
rs11829565	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837316	0.90[AFR][1000 genomes]
rs1492328	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492337	1.00[ASN][1000 genomes]
rs1492338	1.00[ASN][1000 genomes]
rs17128391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128416	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17533321	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598093	1.00[ASN][1000 genomes]
rs17598156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599001	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599042	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844979	1.00[ASN][1000 genomes]
rs1844982	1.00[ASN][1000 genomes]
rs1873674	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992608	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4767980	1.00[ASN][1000 genomes]
rs4768261	1.00[ASN][1000 genomes]
rs4768265	1.00[ASN][1000 genomes]
rs4768287	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768288	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768289	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55642775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649806	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818225	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036709	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211973	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56952712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57161116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59005564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59095251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59367732	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094611	1.00[ASN][1000 genomes]
rs73100423	1.00[ASN][1000 genomes]
rs73100426	0.89[ASN][1000 genomes]
rs73100438	1.00[ASN][1000 genomes]
rs73106618	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106620	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106623	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110070	1.00[ASN][1000 genomes]
rs73110091	1.00[ASN][1000 genomes]
rs73112007	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73112026	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73114281	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73114284	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7315186	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv8970	chr12:40904094-40951213	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3388339	chr12:40917344-40931738	Enhancers Weak transcription	TF binding region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40915600-40919400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:40918600-40919400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:40918800-40919200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:40918800-40919400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:40918800-40919400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:40919000-40919400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:40919000-40919400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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