Variant report

Variant	rs12653042
Chromosome Location	chr5:52108819-52108820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52094605..52098066-chr5:52105462..52108939,4	MCF-7	breast:
2	chr5:52105817..52109193-chr5:52109849..52112036,3	K562	blood:
3	chr5:52102363..52104611-chr5:52106216..52108903,2	MCF-7	breast:
4	chr5:52107198..52108898-chr5:52111929..52113884,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12652120	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13158244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13182946	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13188662	0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13189629	0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454581	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2938796	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6879140	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6883810	0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52099000-52118000	Weak transcription	Right Ventricle	heart
2	chr5:52099600-52110000	Weak transcription	Ovary	ovary
3	chr5:52099600-52112800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:52099800-52112600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:52099800-52118200	Weak transcription	Psoas Muscle	Psoas
6	chr5:52100400-52110000	Weak transcription	HUVEC	blood vessel
7	chr5:52100600-52113400	Enhancers	Colon Smooth Muscle	Colon
8	chr5:52100800-52112800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:52100800-52113200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:52101000-52109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:52101200-52109000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:52101200-52109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:52101400-52110000	Weak transcription	Adipose Nuclei	Adipose
14	chr5:52103000-52112000	Weak transcription	Dnd41	blood
15	chr5:52104800-52110800	Weak transcription	Fetal Lung	lung
16	chr5:52105200-52111200	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:52106200-52109400	Weak transcription	Liver	Liver
18	chr5:52106200-52109800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:52106200-52109800	Weak transcription	Fetal Stomach	stomach
20	chr5:52106200-52109800	Weak transcription	Left Ventricle	heart
21	chr5:52106200-52109800	Weak transcription	Right Atrium	heart
22	chr5:52106200-52115600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:52106200-52132600	Weak transcription	Lung	lung
24	chr5:52106600-52109400	Weak transcription	Spleen	Spleen
25	chr5:52106600-52111400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:52106600-52113800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:52106600-52114600	Weak transcription	Fetal Kidney	kidney
28	chr5:52107200-52109200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:52107200-52110800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:52107400-52109400	Weak transcription	NH-A	brain
31	chr5:52107600-52113600	Weak transcription	HepG2	liver
32	chr5:52107800-52109400	Weak transcription	Hela-S3	cervix
33	chr5:52107800-52109600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:52107800-52109800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:52107800-52110600	Weak transcription	Small Intestine	intestine
36	chr5:52108000-52109400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:52108000-52109600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:52108000-52109600	Weak transcription	NHLF	lung
39	chr5:52108000-52109600	Weak transcription	Osteobl	bone
40	chr5:52108000-52123000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:52108400-52109400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:52108400-52109400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:52108400-52109600	Weak transcription	NHDF-Ad	bronchial
44	chr5:52108600-52109600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:52108800-52109000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr5:52108800-52118400	Weak transcription	Aorta	Aorta

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