Variant report

Variant	rs28709139
Chromosome Location	chr2:33592141-33592142
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	chr2:33496051..33497746-chr2:33589877..33592347,2	MCF-7	breast:
2	chr2:33591629..33594068-chr2:33601379..33603892,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1017677	0.81[ASN][1000 genomes]
rs10198960	0.85[ASN][1000 genomes]
rs11885449	0.84[ASN][1000 genomes]
rs11891105	0.84[ASN][1000 genomes]
rs11892861	0.85[ASN][1000 genomes]
rs17012917	0.80[ASN][1000 genomes]
rs17012922	0.85[ASN][1000 genomes]
rs1869449	0.82[ASN][1000 genomes]
rs2015189	0.82[ASN][1000 genomes]
rs2290426	0.90[ASN][1000 genomes]
rs2305502	0.85[ASN][1000 genomes]
rs28414403	0.99[ASN][1000 genomes]
rs28437398	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34447926	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3769549	0.92[ASN][1000 genomes]
rs3769550	0.87[ASN][1000 genomes]
rs3769552	0.86[ASN][1000 genomes]
rs58804388	0.81[ASN][1000 genomes]
rs59867835	0.83[ASN][1000 genomes]
rs6543707	0.82[ASN][1000 genomes]
rs7566302	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
2	chr2:33558400-33592200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:33578800-33612200	Weak transcription	Fetal Kidney	kidney
4	chr2:33581400-33594400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:33581400-33602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:33581600-33611400	Weak transcription	Fetal Stomach	stomach
7	chr2:33582800-33601800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:33584200-33593400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:33586200-33603600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:33588400-33624400	Weak transcription	Gastric	stomach
11	chr2:33588800-33596000	Weak transcription	Fetal Intestine Small	intestine
12	chr2:33589200-33598000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:33589200-33623000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:33589400-33594800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:33589600-33593000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:33589600-33595000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:33589600-33597600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:33590000-33595200	Weak transcription	K562	blood
19	chr2:33590600-33592400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:33590600-33592600	Enhancers	Brain Hippocampus Middle	brain
21	chr2:33590600-33615800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:33590600-33624800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:33590800-33594400	Weak transcription	Liver	Liver
24	chr2:33590800-33594600	Weak transcription	Aorta	Aorta
25	chr2:33590800-33595000	Weak transcription	Left Ventricle	heart
26	chr2:33590800-33596000	Weak transcription	Esophagus	oesophagus
27	chr2:33590800-33612600	Weak transcription	Ovary	ovary
28	chr2:33591000-33592400	Enhancers	Stomach Smooth Muscle	stomach
29	chr2:33591000-33592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:33591000-33592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:33591200-33592200	Enhancers	HSMM	muscle
32	chr2:33591200-33594400	Weak transcription	NH-A	brain
33	chr2:33591400-33616000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:33591600-33592400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:33591800-33592800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:33591800-33594400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:33591800-33594400	Weak transcription	HMEC	breast
38	chr2:33591800-33595800	Weak transcription	Brain Substantia Nigra	brain
39	chr2:33591800-33595800	Weak transcription	Fetal Lung	lung
40	chr2:33591800-33596000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:33591800-33601800	Weak transcription	NHLF	lung
42	chr2:33592000-33592400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:33592000-33595000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:33592000-33595400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:33592000-33595600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:33592000-33595600	Weak transcription	Fetal Heart	heart
47	chr2:33592000-33595600	Weak transcription	NHDF-Ad	bronchial
48	chr2:33592000-33595800	Weak transcription	Brain Anterior Caudate	brain
49	chr2:33592000-33595800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:33592000-33596200	Weak transcription	Brain Angular Gyrus	brain

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