Variant report

Variant	rs10773599
Chromosome Location	chr12:123297419-123297420
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123296314..123299093-chr12:123319595..123321545,2	K562	blood:
2	chr12:123293432..123295111-chr12:123296025..123298084,2	K562	blood:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1026395	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1037593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10744401	0.80[EUR][1000 genomes]
rs10773627	0.81[YRI][hapmap]
rs10847742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847910	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10848148	1.00[JPT][hapmap]
rs11060142	0.84[AFR][1000 genomes]
rs11060152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060932	1.00[JPT][hapmap]
rs11060999	1.00[JPT][hapmap]
rs12311043	1.00[JPT][hapmap]
rs12367291	0.82[AFR][1000 genomes]
rs12369710	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260121	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12811036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824418	0.82[AFR][1000 genomes]
rs1671681	0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1671682	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1671683	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1696316	0.84[AFR][1000 genomes]
rs1696321	0.83[LWK][hapmap];0.81[YRI][hapmap]
rs1696322	0.92[YRI][hapmap]
rs1696325	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1696355	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs1798560	0.84[AFR][1000 genomes]
rs1798561	0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1798563	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1798565	0.83[AFR][1000 genomes]
rs1798569	0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1975761	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2061099	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2343107	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2456151	0.83[AFR][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2649896	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2649899	0.84[AFR][1000 genomes]
rs2649900	0.84[EUR][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2656812	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2656814	0.84[AFR][1000 genomes]
rs3844369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852535	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038070	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4038080	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038081	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424710	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426165	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4759355	0.81[YRI][hapmap]
rs4759384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4759389	0.81[YRI][hapmap]
rs4759391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6489241	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651683	1.00[JPT][hapmap]
rs7138257	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7305256	0.83[EUR][1000 genomes]
rs7306047	1.00[CHD][hapmap]
rs7306948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7485652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7487095	0.93[EUR][1000 genomes]
rs7957643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958155	1.00[JPT][hapmap]
rs7960548	0.90[AFR][1000 genomes]
rs839354	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs897391	0.81[YRI][hapmap]
rs897393	0.81[YRI][hapmap]
rs921808	0.81[YRI][hapmap]
rs967281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788154	0.88[AFR][1000 genomes]
rs9795629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]

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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10773599	TMEM120B	cis	parietal	SCAN
rs10773599	EIF2B1	cis	parietal	SCAN
rs10773599	KDM2B	cis	cerebellum	SCAN
rs10773599	RAB35	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123259400-123310600	Weak transcription	HSMMtube	muscle
2	chr12:123259800-123310600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:123260000-123303600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:123265600-123303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:123266000-123303800	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:123278600-123305600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:123284800-123297600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:123284800-123297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:123286600-123303600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:123289200-123303800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:123290600-123310400	Weak transcription	Aorta	Aorta
12	chr12:123291800-123304800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:123294200-123297600	Weak transcription	GM12878-XiMat	blood
14	chr12:123296400-123310200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:123297000-123302200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:123297200-123297600	Enhancers	Primary B cells from cord blood	blood
17	chr12:123297400-123297600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:123297400-123298000	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:123297400-123298400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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