Variant report

Variant	rs1199917
Chromosome Location	chr12:83291352-83291353
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	chr12:83290340..83292538-chr12:83294393..83296848,3	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10862518	0.88[ASN][1000 genomes]
rs11115469	0.86[ASN][1000 genomes]
rs1199916	0.93[ASN][1000 genomes]
rs1199918	0.88[ASN][1000 genomes]
rs1199919	0.83[ASN][1000 genomes]
rs1199920	0.88[ASN][1000 genomes]
rs1199921	0.88[ASN][1000 genomes]
rs1208130	0.88[ASN][1000 genomes]
rs12298134	0.88[ASN][1000 genomes]
rs1508645	0.93[ASN][1000 genomes]
rs1508647	0.93[ASN][1000 genomes]
rs1508648	0.89[ASN][1000 genomes]
rs1616906	0.89[ASN][1000 genomes]
rs1703088	0.89[ASN][1000 genomes]
rs1703094	0.88[ASN][1000 genomes]
rs1703097	0.93[ASN][1000 genomes]
rs1703098	0.90[ASN][1000 genomes]
rs1703102	0.94[ASN][1000 genomes]
rs1703110	0.89[ASN][1000 genomes]
rs1796159	0.88[ASN][1000 genomes]
rs1796181	0.88[ASN][1000 genomes]
rs1796182	0.89[ASN][1000 genomes]
rs1796183	0.86[ASN][1000 genomes]
rs1796184	0.89[ASN][1000 genomes]
rs1796185	0.89[ASN][1000 genomes]
rs1796190	0.89[ASN][1000 genomes]
rs1796201	0.88[ASN][1000 genomes]
rs1796202	0.83[ASN][1000 genomes]
rs1796203	0.89[ASN][1000 genomes]
rs1848441	0.88[ASN][1000 genomes]
rs2662077	0.94[ASN][1000 genomes]
rs2733625	0.88[ASN][1000 genomes]
rs34592898	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61931364	0.82[EUR][1000 genomes]
rs6539696	0.88[ASN][1000 genomes]
rs7133985	0.89[ASN][1000 genomes]
rs7134264	0.89[ASN][1000 genomes]
rs7138118	0.89[ASN][1000 genomes]
rs7296706	0.88[ASN][1000 genomes]
rs7299821	0.88[ASN][1000 genomes]
rs7300604	0.88[ASN][1000 genomes]
rs7301010	0.88[ASN][1000 genomes]
rs7304122	0.88[ASN][1000 genomes]
rs7308048	0.89[ASN][1000 genomes]
rs7310705	0.88[ASN][1000 genomes]
rs7314923	0.88[ASN][1000 genomes]
rs73360279	0.82[EUR][1000 genomes]
rs7972978	0.89[ASN][1000 genomes]
rs9788273	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83274400-83304200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:83274600-83298400	Weak transcription	Brain Angular Gyrus	brain
3	chr12:83278200-83313400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:83279000-83336400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:83281000-83306400	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:83282000-83295200	Weak transcription	Fetal Stomach	stomach
7	chr12:83282400-83291800	Weak transcription	Fetal Lung	lung
8	chr12:83282400-83294600	Weak transcription	Fetal Kidney	kidney
9	chr12:83285000-83291400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:83286200-83292400	Weak transcription	Fetal Brain Female	brain
11	chr12:83287400-83292000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:83288000-83292200	Weak transcription	Fetal Heart	heart
13	chr12:83288400-83292000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:83288400-83304200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:83289000-83292400	Weak transcription	Fetal Intestine Large	intestine
16	chr12:83289600-83293200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:83289600-83293200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:83290000-83292000	Weak transcription	Stomach Mucosa	stomach
19	chr12:83290000-83293000	Weak transcription	Ovary	ovary
20	chr12:83290000-83293200	Weak transcription	Esophagus	oesophagus
21	chr12:83290000-83296000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:83290000-83303000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:83290200-83291400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:83290200-83297200	Weak transcription	Gastric	stomach
25	chr12:83290200-83307400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:83290400-83307400	Weak transcription	Fetal Intestine Small	intestine
27	chr12:83290600-83291400	Enhancers	NHEK	skin
28	chr12:83290600-83301000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:83290600-83306000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:83290800-83291600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:83291000-83292400	Weak transcription	Brain Substantia Nigra	brain
32	chr12:83291000-83292400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:83291000-83292600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:83291000-83304000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:83291200-83293600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:83291200-83298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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