Variant report

Variant	rs10880309
Chromosome Location	chr12:42903342-42903343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1008040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785343	0.99[ASN][1000 genomes]
rs10880311	0.96[ASN][1000 genomes]
rs12424992	0.98[ASN][1000 genomes]
rs12822031	0.98[ASN][1000 genomes]
rs1985217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2019557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406678	1.00[ASN][1000 genomes]
rs2406680	1.00[ASN][1000 genomes]
rs2406681	0.98[ASN][1000 genomes]
rs2406682	0.98[ASN][1000 genomes]
rs28491015	1.00[ASN][1000 genomes]
rs28689646	0.96[ASN][1000 genomes]
rs3895894	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9669495	0.98[ASN][1000 genomes]

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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42878600-42904800	Weak transcription	Right Atrium	heart
2	chr12:42885400-42913600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:42886800-42904800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:42890600-42905800	Weak transcription	Osteobl	bone
5	chr12:42891000-42910200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:42898400-42914000	Weak transcription	NH-A	brain
7	chr12:42898400-42929000	Weak transcription	Fetal Kidney	kidney
8	chr12:42898600-42904400	Weak transcription	HUVEC	blood vessel
9	chr12:42898600-42910400	Weak transcription	Fetal Stomach	stomach
10	chr12:42899000-42910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:42900600-42903400	Enhancers	Fetal Heart	heart
12	chr12:42901200-42905800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:42901400-42905200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:42901600-42904600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:42901600-42904600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:42901600-42940200	Weak transcription	Ovary	ovary
17	chr12:42902400-42903400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:42902400-42903400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:42902400-42903400	Enhancers	Aorta	Aorta
20	chr12:42902400-42903400	Enhancers	Fetal Muscle Leg	muscle
21	chr12:42902600-42903400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:42902600-42903400	Enhancers	Brain Angular Gyrus	brain
23	chr12:42902600-42903400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr12:42902600-42903400	Enhancers	Rectal Smooth Muscle	rectum
25	chr12:42902600-42903400	Enhancers	Right Ventricle	heart
26	chr12:42902600-42904800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:42902800-42903400	Enhancers	HSMMtube	muscle
28	chr12:42903000-42903400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:42903000-42903400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:42903000-42904600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:42903000-42913400	Weak transcription	HMEC	breast
32	chr12:42903200-42903400	Enhancers	Left Ventricle	heart
33	chr12:42903200-42905000	Weak transcription	Stomach Smooth Muscle	stomach

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