Variant report

Variant	rs10879831
Chromosome Location	chr12:41582603-41582604
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10748267	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879858	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879867	0.91[ASN][1000 genomes]
rs12829840	0.85[ASN][1000 genomes]
rs1367602	0.85[EUR][1000 genomes]
rs1431104	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1431110	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1431112	0.91[ASN][1000 genomes]
rs1461094	0.85[EUR][1000 genomes]
rs1864611	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1864613	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163415	0.84[EUR][1000 genomes]
rs2163416	0.83[ASN][1000 genomes]
rs2169299	0.84[EUR][1000 genomes]
rs281832	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs281837	0.80[EUR][1000 genomes]
rs281839	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs281840	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs281841	0.84[EUR][1000 genomes]
rs281843	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3847980	0.85[EUR][1000 genomes]
rs3847981	0.85[EUR][1000 genomes]
rs3858726	0.85[EUR][1000 genomes]
rs4238081	0.88[ASN][1000 genomes]
rs4767999	0.88[ASN][1000 genomes]
rs4768334	0.83[ASN][1000 genomes]
rs6582240	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7303285	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7305919	0.85[ASN][1000 genomes]
rs776560	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs776561	0.84[EUR][1000 genomes]
rs776562	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs776567	0.81[EUR][1000 genomes]
rs7954881	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963760	0.88[ASN][1000 genomes]
rs975602	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1048124	chr12:41499221-41585315	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a
5	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41581200-41585200	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:41581400-41584400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:41581600-41583600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:41581600-41583800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:41581600-41584200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:41581600-41584400	Active TSS	Rectal Smooth Muscle	rectum
7	chr12:41581800-41582800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:41581800-41582800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:41581800-41583000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:41581800-41583000	Active TSS	Brain Hippocampus Middle	brain
11	chr12:41581800-41583000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:41581800-41583000	Bivalent Enhancer	Fetal Brain Male	brain
13	chr12:41581800-41583400	Active TSS	Brain Anterior Caudate	brain
14	chr12:41581800-41583800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr12:41581800-41584000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:41581800-41584200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr12:41581800-41584200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr12:41581800-41584400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:41581800-41584600	Active TSS	Brain Substantia Nigra	brain
20	chr12:41581800-41585200	Active TSS	Colon Smooth Muscle	Colon
21	chr12:41582000-41582800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:41582000-41582800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr12:41582000-41583000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:41582000-41583000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:41582000-41583200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr12:41582000-41583200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr12:41582000-41583600	Bivalent/Poised TSS	A549	lung
28	chr12:41582000-41583800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:41582000-41583800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:41582000-41583800	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:41582000-41584000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:41582000-41584000	Bivalent/Poised TSS	Colonic Mucosa	Colon
33	chr12:41582000-41584200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
34	chr12:41582000-41584200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr12:41582000-41584200	Active TSS	Right Atrium	heart
36	chr12:41582000-41584400	Active TSS	Aorta	Aorta
37	chr12:41582000-41584400	Bivalent Enhancer	Fetal Heart	heart
38	chr12:41582200-41583400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr12:41582200-41583600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
40	chr12:41582200-41584000	Active TSS	Brain Angular Gyrus	brain
41	chr12:41582200-41584000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
42	chr12:41582200-41584200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
43	chr12:41582400-41582800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
44	chr12:41582400-41582800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:41582400-41582800	Bivalent/Poised TSS	Fetal Brain Female	brain
46	chr12:41582400-41582800	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr12:41582400-41582800	Enhancers	Placenta	Placenta
48	chr12:41582400-41582800	Bivalent Enhancer	HUVEC	blood vessel
49	chr12:41582400-41582800	Bivalent/Poised TSS	NHEK	skin
50	chr12:41582400-41583000	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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