Variant report

Variant	rs13088659
Chromosome Location	chr3:145812636-145812637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145804487..145808112-chr3:145810682..145813494,3	MCF-7	breast:
2	chr3:145809706..145813373-chr3:145877406..145880433,4	MCF-7	breast:
3	chr3:145810461..145813616-chr3:145877675..145880858,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13065572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13066226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13075648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13095139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16857900	0.97[EUR][1000 genomes]
rs34041519	0.87[AMR][1000 genomes]
rs34092280	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34201307	1.00[AFR][1000 genomes]
rs34248972	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34298175	1.00[AMR][1000 genomes]
rs34392701	1.00[AFR][1000 genomes]
rs34589717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34695557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34901222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35017529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35020806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35080774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35479343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35520151	1.00[AFR][1000 genomes]
rs35687630	1.00[AFR][1000 genomes]
rs35880277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35969739	1.00[AMR][1000 genomes]
rs62272613	1.00[AFR][1000 genomes]
rs71300372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71300373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71300374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71300375	0.81[EUR][1000 genomes]
rs71300377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71300378	1.00[AMR][1000 genomes]
rs71300379	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71300380	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71300381	1.00[AFR][1000 genomes]
rs71300383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71621137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
3	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
4	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
6	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
8	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
9	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
15	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
16	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
17	chr3:145794400-145815600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:145794400-145818200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:145794400-145818800	Weak transcription	Ovary	ovary
20	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:145794600-145819200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:145796200-145821400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:145798000-145818400	Weak transcription	HSMMtube	muscle
25	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:145804000-145819200	Weak transcription	NH-A	brain
27	chr3:145804600-145818000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
29	chr3:145809000-145818200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:145809200-145821600	Weak transcription	HMEC	breast
31	chr3:145809600-145817200	Weak transcription	Fetal Intestine Small	intestine
32	chr3:145810200-145823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:145810400-145816400	Weak transcription	Brain Substantia Nigra	brain
34	chr3:145810400-145817800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:145810400-145829000	Weak transcription	NHLF	lung
36	chr3:145810400-145830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:145810600-145815600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:145810600-145818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:145810600-145827200	Weak transcription	Small Intestine	intestine
41	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:145812000-145813200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:145812000-145815600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:145812000-145815600	Weak transcription	Adipose Nuclei	Adipose
45	chr3:145812000-145818600	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:145812000-145818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:145812000-145826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:145812000-145826800	Weak transcription	Aorta	Aorta
49	chr3:145812200-145813600	Weak transcription	HSMM	muscle
50	chr3:145812200-145815800	Weak transcription	Osteobl	bone

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