Variant report

Variant	rs1199920
Chromosome Location	chr12:83277870-83277871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:83276930..83278869-chr12:83287906..83289441,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10862518	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11115469	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1199916	0.95[ASN][1000 genomes]
rs1199917	0.88[ASN][1000 genomes]
rs1199918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199919	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs1199921	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298134	1.00[ASN][1000 genomes]
rs1508645	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1508647	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1508648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1616906	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1703088	0.98[ASN][1000 genomes]
rs1703094	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703097	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1703098	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1703102	0.83[ASN][1000 genomes]
rs1703110	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1796159	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1796181	1.00[ASN][1000 genomes]
rs1796182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1796183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1796184	0.98[ASN][1000 genomes]
rs1796185	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs1796190	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796201	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796202	0.95[ASN][1000 genomes]
rs1796203	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1848441	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2662077	0.83[ASN][1000 genomes]
rs2733625	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34592898	0.88[ASN][1000 genomes]
rs6539696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7133985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7134264	0.98[ASN][1000 genomes]
rs7296706	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7299821	1.00[ASN][1000 genomes]
rs7300604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7301010	1.00[ASN][1000 genomes]
rs7304122	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7308048	0.98[ASN][1000 genomes]
rs7310705	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7314923	1.00[ASN][1000 genomes]
rs7972978	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83242200-83289800	Weak transcription	Stomach Mucosa	stomach
2	chr12:83262200-83278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:83264600-83278000	Weak transcription	Small Intestine	intestine
4	chr12:83274400-83304200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:83274600-83280000	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:83274600-83280400	Weak transcription	Fetal Lung	lung
7	chr12:83274600-83284200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:83274600-83286000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:83274600-83298400	Weak transcription	Brain Angular Gyrus	brain
10	chr12:83274800-83282800	Weak transcription	Fetal Brain Female	brain
11	chr12:83276800-83278600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:83277200-83278000	Enhancers	Brain Substantia Nigra	brain
13	chr12:83277200-83278200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:83277200-83278400	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:83277400-83278000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:83277400-83278200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:83277400-83278200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:83277600-83278000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:83277600-83278000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:83277600-83278200	Enhancers	Brain Hippocampus Middle	brain
21	chr12:83277800-83278000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:83277800-83278000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:83277800-83278000	Active TSS	Brain Anterior Caudate	brain
24	chr12:83277800-83278200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr12:83277800-83278200	Enhancers	Fetal Brain Male	brain
26	chr12:83277800-83282600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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