Variant report

Variant	rs61943518
Chromosome Location	chr12:118562144-118562145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr12:118562104-118562783	HepG2	liver:	n/a	n/a
2	FOXA2	chr12:118561986-118563014	HepG2	liver:	n/a	chr12:118562448-118562460
3	EP300	chr12:118562126-118562796	HepG2	liver:	n/a	chr12:118562451-118562461
4	NR2F2	chr12:118562121-118562721	MCF-7	breast:	n/a	n/a
5	MYBL2	chr12:118562124-118562755	HepG2	liver:	n/a	n/a
6	NR2F2	chr12:118562129-118562753	HepG2	liver:	n/a	n/a
7	MAX	chr12:118562082-118562674	HepG2	liver:	n/a	n/a
8	NR2F2	chr12:118562077-118562790	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
VSIG10	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12423154	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423959	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017414	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2936840	0.86[ASN][1000 genomes]
rs3847652	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56070243	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61943519	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61943521	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73217996	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956285	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961197	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970036	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542400-118562400	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:118542400-118569400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:118542600-118569400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:118545400-118569600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:118546400-118569400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:118548600-118563400	Weak transcription	Left Ventricle	heart
9	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
11	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
12	chr12:118554400-118566000	Weak transcription	Small Intestine	intestine
13	chr12:118554800-118564000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:118557800-118564000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:118558200-118564000	Enhancers	HepG2	liver
16	chr12:118558800-118564000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:118558800-118572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:118559000-118565600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:118559000-118569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:118559200-118564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:118559200-118564000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:118559200-118566600	Weak transcription	Fetal Lung	lung
23	chr12:118559200-118567200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:118559200-118569400	Weak transcription	Adipose Nuclei	Adipose
25	chr12:118559200-118569400	Weak transcription	Dnd41	blood
26	chr12:118559200-118569600	Weak transcription	GM12878-XiMat	blood
27	chr12:118559200-118569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:118559200-118570000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:118559200-118572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:118559200-118572600	Weak transcription	NHEK	skin
31	chr12:118559200-118572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:118559200-118573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:118559200-118573000	Weak transcription	Fetal Kidney	kidney
34	chr12:118559200-118573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:118559200-118573400	Weak transcription	Fetal Intestine Small	intestine
36	chr12:118559400-118562200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:118559400-118562200	Weak transcription	K562	blood
38	chr12:118559400-118562600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:118559400-118564000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:118559400-118564000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:118559400-118567400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:118559400-118569200	Weak transcription	Brain Substantia Nigra	brain
43	chr12:118559400-118569200	Weak transcription	A549	lung
44	chr12:118559400-118569400	Weak transcription	Brain Anterior Caudate	brain
45	chr12:118559400-118569400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:118559400-118569800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:118559400-118572600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:118559400-118572800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:118559600-118562200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:118559800-118564000	Weak transcription	Ovary	ovary

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