Variant report

Variant	rs12478460
Chromosome Location	chr2:149072438-149072439
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12463445	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464464	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466152	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474162	0.88[EUR][1000 genomes]
rs12474340	0.88[EUR][1000 genomes]
rs12474357	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2382212	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56990703	0.91[AFR][1000 genomes]
rs59059734	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59745578	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73965305	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578733	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
3	chr2:149056000-149076400	Weak transcription	Esophagus	oesophagus
4	chr2:149058600-149076400	Weak transcription	Aorta	Aorta
5	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:149063400-149080600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:149063800-149073800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:149067200-149095800	Weak transcription	HSMM	muscle
10	chr2:149068400-149073200	Weak transcription	Adipose Nuclei	Adipose
11	chr2:149069000-149075600	Weak transcription	Fetal Intestine Large	intestine
12	chr2:149069200-149096400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:149069400-149077800	Weak transcription	Gastric	stomach
14	chr2:149069400-149096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:149069600-149075600	Weak transcription	Spleen	Spleen
17	chr2:149069800-149076400	Weak transcription	Right Ventricle	heart
18	chr2:149070400-149075600	Weak transcription	Fetal Lung	lung
19	chr2:149070600-149072800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:149071000-149078000	Weak transcription	Pancreas	Pancrea
21	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
22	chr2:149071200-149073000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:149071200-149074400	Weak transcription	Brain Germinal Matrix	brain
24	chr2:149071200-149075000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:149071200-149077200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:149071400-149073000	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:149071400-149073600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:149071400-149073800	Weak transcription	Fetal Intestine Small	intestine
29	chr2:149071400-149074800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:149071400-149100400	Weak transcription	Ovary	ovary
31	chr2:149071600-149075400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:149071600-149078600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:149071600-149094000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:149071800-149095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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