Variant report

Variant	rs12470507
Chromosome Location	chr2:55383624-55383625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55366215..55370139-chr2:55381125..55383848,4	K562	blood:
2	chr2:55275586..55279731-chr2:55383502..55386447,3	K562	blood:
3	chr2:55378428..55381284-chr2:55382487..55384417,2	MCF-7	breast:
4	chr2:55381461..55384180-chr2:55385114..55387794,2	MCF-7	breast:
5	chr2:18390509..18393280-chr2:55382468..55384962,2	MCF-7	breast:
6	chr2:55272933..55279731-chr2:55382949..55387132,8	K562	blood:
7	chr2:55275348..55277918-chr2:55382981..55385901,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11694920	1.00[YRI][hapmap]
rs12465548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1561231	1.00[YRI][hapmap]
rs17039586	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17046586	1.00[YRI][hapmap]
rs2118283	1.00[YRI][hapmap]
rs2164715	1.00[YRI][hapmap]
rs2230370	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2589081	1.00[YRI][hapmap]
rs2589082	1.00[YRI][hapmap]
rs35202112	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233959	1.00[YRI][hapmap]
rs4591380	1.00[YRI][hapmap]
rs6545476	1.00[YRI][hapmap]
rs6545479	1.00[YRI][hapmap]
rs66479307	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719303	0.82[GIH][hapmap]
rs6723870	1.00[YRI][hapmap]
rs6730950	0.82[GIH][hapmap]
rs72797538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72797544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72797555	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72797558	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72797572	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72797589	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72797591	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72797593	0.89[AMR][1000 genomes]
rs72797598	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72799509	0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55376000-55383800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:55378000-55386800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55378000-55386800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:55378200-55386200	Enhancers	Brain Hippocampus Middle	brain
5	chr2:55378200-55388000	Enhancers	Brain Cingulate Gyrus	brain
6	chr2:55378200-55388800	Enhancers	Adipose Nuclei	Adipose
7	chr2:55378400-55383800	Enhancers	NHLF	lung
8	chr2:55378600-55385600	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:55378600-55386800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr2:55378600-55386800	Enhancers	Fetal Stomach	stomach
11	chr2:55378800-55385600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55378800-55386800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:55379000-55384200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:55379200-55385200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:55379400-55385200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:55379400-55386600	Enhancers	Fetal Intestine Large	intestine
17	chr2:55379400-55387000	Enhancers	Fetal Intestine Small	intestine
18	chr2:55379600-55385000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:55379600-55386800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:55380000-55384400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:55380200-55386000	Enhancers	Hela-S3	cervix
22	chr2:55380400-55384400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55380600-55383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55380600-55384000	Enhancers	Fetal Heart	heart
25	chr2:55380600-55384000	Enhancers	HMEC	breast
26	chr2:55380800-55385400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55381000-55384400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:55381000-55387800	Enhancers	Fetal Muscle Leg	muscle
29	chr2:55381000-55391000	Enhancers	Stomach Mucosa	stomach
30	chr2:55381200-55390600	Enhancers	Brain Angular Gyrus	brain
31	chr2:55381400-55385600	Enhancers	Brain Germinal Matrix	brain
32	chr2:55381600-55383800	Weak transcription	Fetal Thymus	thymus
33	chr2:55381600-55386800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:55381600-55386800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:55381800-55384400	Weak transcription	GM12878-XiMat	blood
36	chr2:55381800-55385200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:55381800-55385600	Enhancers	NHEK	skin
38	chr2:55381800-55387200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:55382000-55383800	Weak transcription	Spleen	Spleen
40	chr2:55382000-55384000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:55382000-55385000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:55382000-55385200	Enhancers	Fetal Lung	lung
43	chr2:55382000-55385400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:55382200-55384000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:55382200-55384600	Weak transcription	Colonic Mucosa	Colon
46	chr2:55382200-55385400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:55382200-55385400	Bivalent Enhancer	HepG2	liver
48	chr2:55382400-55383800	Weak transcription	Right Atrium	heart
49	chr2:55382400-55384200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr2:55382400-55384200	Weak transcription	Monocytes-CD14+_RO01746	blood

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