Variant report

Variant	rs3794529
Chromosome Location	chr15:52061940-52061941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52041772..52043796-chr15:52059873..52062736,2	MCF-7	breast:
2	chr15:52043955..52045654-chr15:52058986..52062034,3	MCF-7	breast:
3	chr15:52054450..52058295-chr15:52061213..52063877,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000259377	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1350173	0.85[EUR][1000 genomes]
rs16953082	0.88[EUR][1000 genomes]
rs16964486	0.88[EUR][1000 genomes]
rs16964488	0.85[EUR][1000 genomes]
rs16964505	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964506	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964507	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964508	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964510	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964518	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs16964528	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16964532	0.88[EUR][1000 genomes]
rs16964555	0.83[EUR][1000 genomes]
rs16964561	0.83[EUR][1000 genomes]
rs16964579	0.83[EUR][1000 genomes]
rs16964585	0.83[EUR][1000 genomes]
rs16964596	0.83[EUR][1000 genomes]
rs17705373	0.95[EUR][1000 genomes]
rs3751595	0.88[EUR][1000 genomes]
rs4775971	0.98[EUR][1000 genomes]
rs56221158	0.90[EUR][1000 genomes]
rs60398357	0.85[EUR][1000 genomes]
rs7165594	0.88[EUR][1000 genomes]
rs7166954	0.93[EUR][1000 genomes]
rs7167759	0.88[EUR][1000 genomes]
rs7174616	0.85[EUR][1000 genomes]
rs7175121	0.85[EUR][1000 genomes]
rs7179971	0.93[EUR][1000 genomes]
rs7180093	0.93[EUR][1000 genomes]
rs73405349	0.85[EUR][1000 genomes]
rs73405355	0.85[EUR][1000 genomes]
rs73405356	0.85[EUR][1000 genomes]
rs73405364	0.87[EUR][1000 genomes]
rs73405388	0.85[EUR][1000 genomes]
rs7342575	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74015721	0.85[EUR][1000 genomes]
rs74015757	0.98[EUR][1000 genomes]
rs74015761	0.98[EUR][1000 genomes]
rs7496198	0.81[EUR][1000 genomes]
rs8036648	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
4	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
6	chr15:52052200-52068600	Weak transcription	HMEC	breast
7	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
9	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
10	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
12	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
13	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:52052600-52065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:52052600-52106600	Weak transcription	HSMM	muscle
16	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
17	chr15:52058400-52064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:52058400-52067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52058600-52068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:52060000-52062600	Strong transcription	Fetal Brain Female	brain
22	chr15:52060000-52063000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:52060000-52063000	Strong transcription	Fetal Stomach	stomach
24	chr15:52060000-52063200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr15:52060000-52063600	Strong transcription	Ovary	ovary
26	chr15:52060200-52062400	Strong transcription	Brain Hippocampus Middle	brain
27	chr15:52060200-52062600	Strong transcription	Aorta	Aorta
28	chr15:52060200-52062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:52060200-52068200	Weak transcription	Liver	Liver
30	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:52060400-52062200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr15:52060400-52062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:52060400-52062400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:52060400-52063600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:52060400-52064600	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:52060400-52068400	Strong transcription	Thymus	Thymus
37	chr15:52060400-52069200	Weak transcription	Placenta	Placenta
38	chr15:52060400-52069800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr15:52060400-52079200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
41	chr15:52060600-52062200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:52060600-52062400	Strong transcription	Brain Anterior Caudate	brain
43	chr15:52060600-52062600	Weak transcription	Brain Germinal Matrix	brain
44	chr15:52060600-52062600	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr15:52060600-52062800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:52060600-52063200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:52060600-52063200	Weak transcription	K562	blood
48	chr15:52060600-52064000	Weak transcription	HUVEC	blood vessel
49	chr15:52060600-52064200	Weak transcription	Right Atrium	heart
50	chr15:52060600-52065200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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