Variant report

Variant	rs12468725
Chromosome Location	chr2:149093863-149093864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10180998	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10196111	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11693638	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13393889	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs13413580	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16828556	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16828570	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2204324	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59052051	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183966	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6734519	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6744194	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72857680	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7563648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750419	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	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
5	nsv1012123	chr2:149078500-149151358	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv583289	chr2:149091754-149170115	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:149067200-149095800	Weak transcription	HSMM	muscle
5	chr2:149069200-149096400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:149069400-149096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
9	chr2:149071400-149100400	Weak transcription	Ovary	ovary
10	chr2:149071600-149094000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:149071800-149095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:149079800-149094000	Weak transcription	Left Ventricle	heart
14	chr2:149085400-149100400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:149086400-149099600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:149086400-149099800	Weak transcription	GM12878-XiMat	blood
17	chr2:149086800-149094000	Weak transcription	Dnd41	blood
18	chr2:149086800-149098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:149086800-149100400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:149088400-149100400	Weak transcription	Fetal Kidney	kidney
21	chr2:149088800-149096200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:149089000-149094000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:149089200-149119400	Weak transcription	Fetal Intestine Small	intestine
24	chr2:149089600-149100400	Weak transcription	Fetal Intestine Large	intestine
25	chr2:149089600-149105400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:149089800-149096000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:149090000-149104200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:149090400-149094000	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:149090400-149094000	Weak transcription	Fetal Stomach	stomach
30	chr2:149090400-149100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:149090400-149100400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:149090600-149096200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:149090600-149100200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:149091000-149100000	Weak transcription	Pancreas	Pancrea
35	chr2:149091800-149094400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:149092200-149094000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:149092400-149094000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:149092400-149094000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:149092400-149095800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:149092400-149100400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:149092400-149100400	Weak transcription	Right Ventricle	heart
42	chr2:149092600-149095600	Weak transcription	Brain Germinal Matrix	brain
43	chr2:149092600-149100400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:149092600-149100400	Weak transcription	Adipose Nuclei	Adipose
45	chr2:149092600-149100400	Weak transcription	Brain Angular Gyrus	brain
46	chr2:149092600-149100400	Weak transcription	Fetal Brain Female	brain
47	chr2:149092600-149100400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:149092600-149100400	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:149092600-149100400	Weak transcription	Small Intestine	intestine
50	chr2:149092800-149100400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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