Variant report

Variant	rs1798561
Chromosome Location	chr12:123300571-123300572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123299469..123302260-chr12:123317882..123320473,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10773599	0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10773627	0.81[YRI][hapmap]
rs10847742	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs10847749	0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10847751	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10847775	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11060152	0.84[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12369710	0.82[AFR][1000 genomes]
rs12811036	0.84[AFR][1000 genomes]
rs1619142	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1671681	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1671682	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1671683	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1696316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1696321	0.91[LWK][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes]
rs1696322	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1696325	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1798560	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1798565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1798569	0.87[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456151	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2649899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2656814	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3844369	0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3852535	0.84[AFR][1000 genomes]
rs4038070	0.86[AFR][1000 genomes]
rs4038080	0.84[AFR][1000 genomes]
rs4038081	0.83[AFR][1000 genomes]
rs4307760	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4424710	0.84[AFR][1000 genomes]
rs4759355	0.81[YRI][hapmap]
rs4759389	0.80[YRI][hapmap]
rs4759391	0.86[AFR][1000 genomes]
rs55650312	0.88[EUR][1000 genomes]
rs55716280	1.00[EUR][1000 genomes]
rs56260598	0.80[EUR][1000 genomes]
rs56294931	0.80[EUR][1000 genomes]
rs59058900	0.96[EUR][1000 genomes]
rs59769449	0.96[EUR][1000 genomes]
rs73415582	1.00[EUR][1000 genomes]
rs7957643	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs897391	0.81[YRI][hapmap]
rs897393	0.81[YRI][hapmap]
rs921808	0.81[YRI][hapmap]
rs967281	0.88[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9795629	0.86[LWK][hapmap];0.82[MKK][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

No data

Chromatin state (count:18 , 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	chr12:123286600-123303600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:123289200-123303800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:123290600-123310400	Weak transcription	Aorta	Aorta
10	chr12:123291800-123304800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:123296400-123310200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:123297000-123302200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:123298000-123301000	Enhancers	Primary B cells from peripheral blood	blood
14	chr12:123298000-123303600	Weak transcription	Fetal Brain Female	brain
15	chr12:123298000-123310600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:123298400-123310400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:123299600-123300600	Weak transcription	Primary B cells from cord blood	blood
18	chr12:123299600-123310600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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