Variant report

Variant	rs12476783
Chromosome Location	chr2:39754150-39754151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39749162..39751923-chr2:39751985..39754949,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10180761	1.00[CHD][hapmap]
rs11900495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475209	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs12476899	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13420542	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1526025	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466784	0.82[AMR][1000 genomes]
rs17473802	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs35368235	1.00[ASN][1000 genomes]
rs72803106	0.83[EUR][1000 genomes]
rs7594967	1.00[YRI][hapmap];0.81[AFR][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	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39749400-39757200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:39749400-39758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:39749400-39761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:39750000-39761000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:39750600-39754400	Enhancers	HepG2	liver
6	chr2:39750800-39760200	Weak transcription	Gastric	stomach
7	chr2:39751200-39760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:39751400-39760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:39751600-39757200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:39751800-39757000	Weak transcription	HUVEC	blood vessel
11	chr2:39752000-39755000	Enhancers	GM12878-XiMat	blood
12	chr2:39752000-39755200	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:39752000-39756600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:39752200-39755200	Enhancers	Primary B cells from cord blood	blood
15	chr2:39752400-39757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:39752600-39756600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:39752600-39756600	Weak transcription	NHDF-Ad	bronchial
18	chr2:39752600-39757000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:39752600-39757000	Weak transcription	NHEK	skin
20	chr2:39752600-39757000	Weak transcription	Osteobl	bone
21	chr2:39752600-39757200	Weak transcription	Hela-S3	cervix
22	chr2:39752600-39757200	Weak transcription	NHLF	lung
23	chr2:39752600-39760400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:39752600-39760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:39752800-39757000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:39753000-39756800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:39753000-39757000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:39753000-39757000	Weak transcription	HSMM	muscle
29	chr2:39753000-39758000	Weak transcription	Placenta	Placenta
30	chr2:39753200-39754200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:39753200-39757000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:39753200-39760200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:39753400-39755800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:39753400-39756000	Weak transcription	Left Ventricle	heart
35	chr2:39753400-39757200	Weak transcription	Fetal Heart	heart
36	chr2:39753400-39757400	Weak transcription	Adipose Nuclei	Adipose
37	chr2:39753400-39757400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:39753400-39757600	Weak transcription	NH-A	brain
39	chr2:39753400-39758000	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:39753400-39761000	Weak transcription	HSMMtube	muscle
41	chr2:39753400-39768400	Weak transcription	Right Ventricle	heart
42	chr2:39753400-39768600	Weak transcription	Right Atrium	heart
43	chr2:39753600-39758200	Weak transcription	Lung	lung
44	chr2:39753600-39767000	Weak transcription	Psoas Muscle	Psoas
45	chr2:39754000-39754200	Enhancers	Skeletal Muscle Male	skeletal muscle

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