Variant report

Variant	rs4142996
Chromosome Location	chr12:59276930-59276931
allele	C/T
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	NANOG	chr12:59276621-59276944	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr12:59276563-59276932	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXP2	chr12:59276596-59276936	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
LRIG3	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13377741	1.00[EUR][1000 genomes]
rs74099549	0.87[ASN][1000 genomes]
rs74099578	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59260600-59284200	Strong transcription	HUVEC	blood vessel
2	chr12:59261400-59284200	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr12:59261600-59284200	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr12:59261800-59280800	Strong transcription	Fetal Intestine Large	intestine
5	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:59263200-59277000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:59263400-59281400	Strong transcription	NHEK	skin
8	chr12:59263600-59278800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:59264800-59284200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:59265000-59277200	Weak transcription	GM12878-XiMat	blood
11	chr12:59265400-59284200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:59266000-59282000	Strong transcription	Adipose Nuclei	Adipose
13	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
14	chr12:59266200-59278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:59266200-59284000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:59266400-59277600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:59266400-59277600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:59266400-59284000	Strong transcription	Fetal Muscle Leg	muscle
19	chr12:59267800-59281600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:59271200-59278200	Weak transcription	Small Intestine	intestine
21	chr12:59271600-59278800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:59271600-59280400	Strong transcription	Liver	Liver
23	chr12:59271600-59281400	Strong transcription	HMEC	breast
24	chr12:59271600-59282000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:59271600-59282000	Strong transcription	NHDF-Ad	bronchial
26	chr12:59271600-59284600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:59271600-59284600	Strong transcription	Osteobl	bone
28	chr12:59271800-59277400	Weak transcription	Fetal Brain Male	brain
29	chr12:59271800-59281400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:59271800-59284000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr12:59272000-59282000	Strong transcription	NHLF	lung
32	chr12:59272200-59281400	Strong transcription	NH-A	brain
33	chr12:59272800-59285800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:59273000-59281400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:59273200-59283400	Weak transcription	Esophagus	oesophagus
36	chr12:59273400-59281200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:59273600-59277200	Weak transcription	Brain Angular Gyrus	brain
38	chr12:59273600-59287000	Weak transcription	Stomach Mucosa	stomach
39	chr12:59273800-59278400	Weak transcription	Psoas Muscle	Psoas
40	chr12:59273800-59280000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:59273800-59283400	Weak transcription	Lung	lung
42	chr12:59273800-59283400	Weak transcription	Spleen	Spleen
43	chr12:59273800-59289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:59274000-59279600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:59274600-59278000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:59274600-59278400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:59274600-59278400	Weak transcription	Fetal Heart	heart
48	chr12:59274600-59278400	Weak transcription	HSMM	muscle
49	chr12:59274600-59278600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:59274600-59279000	Enhancers	Brain Germinal Matrix	brain

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