Variant report

Variant	rs892540
Chromosome Location	chr12:83417475-83417476
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	chr12:83415930..83418702-chr12:83439696..83442546,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10506886	0.85[EUR][1000 genomes]
rs10506887	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10746265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778931	0.91[JPT][hapmap]
rs10862545	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10862546	0.85[EUR][1000 genomes]
rs10862548	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10862550	0.86[EUR][1000 genomes]
rs10862551	0.86[EUR][1000 genomes]
rs10862552	0.86[EUR][1000 genomes]
rs10862553	0.85[EUR][1000 genomes]
rs10862554	0.86[EUR][1000 genomes]
rs10862555	0.86[EUR][1000 genomes]
rs10862556	0.86[EUR][1000 genomes]
rs10862559	0.85[EUR][1000 genomes]
rs10862560	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10862561	0.84[EUR][1000 genomes]
rs10862563	0.84[EUR][1000 genomes]
rs10862564	0.85[EUR][1000 genomes]
rs10862565	0.85[EUR][1000 genomes]
rs10862566	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10862567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862568	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs10862569	0.83[EUR][1000 genomes]
rs10862570	0.85[EUR][1000 genomes]
rs11115526	0.85[EUR][1000 genomes]
rs11115527	0.91[JPT][hapmap]
rs11115534	0.86[EUR][1000 genomes]
rs11115535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11115539	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11115542	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11115543	0.85[EUR][1000 genomes]
rs11115544	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11115545	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11115548	0.84[EUR][1000 genomes]
rs11115549	0.84[EUR][1000 genomes]
rs11115550	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1434423	0.85[EUR][1000 genomes]
rs1434424	0.85[EUR][1000 genomes]
rs17010499	0.86[EUR][1000 genomes]
rs1836248	0.85[EUR][1000 genomes]
rs2020370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[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]
rs2403055	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4144978	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374000	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4387423	0.91[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4387424	0.86[EUR][1000 genomes]
rs7962681	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs7965643	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv1047239	chr12:83362299-83444855	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	nsv523902	chr12:83417475-83423340	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83404400-83420800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:83404400-83422000	Weak transcription	Esophagus	oesophagus
3	chr12:83405000-83436200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:83410600-83421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:83411000-83421000	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:83411000-83435800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:83411200-83418400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:83411200-83422800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:83411400-83423200	Weak transcription	Stomach Mucosa	stomach
10	chr12:83412200-83421200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:83412600-83424400	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:83412800-83422800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:83413600-83421200	Weak transcription	Fetal Lung	lung
14	chr12:83415200-83417600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:83415200-83424600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:83416400-83421000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:83417200-83417600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:83417200-83417600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:83417200-83417600	Enhancers	Fetal Muscle Leg	muscle
20	chr12:83417200-83417600	Strong transcription	Fetal Stomach	stomach
21	chr12:83417200-83418400	Enhancers	Fetal Heart	heart
22	chr12:83417400-83417600	Weak transcription	Pancreas	Pancrea

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