Variant report

Variant	rs352605
Chromosome Location	chr5:106893142-106893143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:106892732..106894780-chr5:106905929..106907820,4	MCF-7	breast:
2	chr5:106893133..106894878-chr5:107007816..107009967,2	MCF-7	breast:
3	chr5:106878075..106880996-chr5:106890627..106894007,3	MCF-7	breast:
4	chr5:106892887..106893840-chr5:106907159..106908105,3	MCF-7	breast:
5	chr5:106891290..106894903-chr5:107005448..107008680,4	MCF-7	breast:
6	chr5:106892845..106895575-chr5:106898409..106900796,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184349	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11957374	0.88[JPT][hapmap]
rs163888	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs163895	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17160159	0.88[JPT][hapmap]
rs17414033	0.82[JPT][hapmap]
rs1966892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1966893	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs388016	1.00[CHB][hapmap]
rs395561	1.00[CHB][hapmap]
rs446774	1.00[CHB][hapmap]
rs6879279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6882355	0.88[JPT][hapmap]
rs6883713	0.88[JPT][hapmap]
rs6884705	0.88[JPT][hapmap]
rs7443170	1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs848827	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2036103	chr5:106892820-106893223	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3517808	chr5:106892843-106893207	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs352605	SLC25A46	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106879000-106899200	Weak transcription	Fetal Stomach	stomach
2	chr5:106881600-106899600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:106884600-106896400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106885600-106893200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:106885600-106894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:106885600-106896400	Weak transcription	Right Atrium	heart
7	chr5:106887200-106899400	Weak transcription	Fetal Lung	lung
8	chr5:106887200-106906800	Weak transcription	Right Ventricle	heart
9	chr5:106889400-106903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:106890000-106895000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:106890000-106895000	Enhancers	NHEK	skin
12	chr5:106890000-106898000	Enhancers	Fetal Heart	heart
13	chr5:106890200-106893600	Enhancers	HSMM	muscle
14	chr5:106890200-106900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:106890400-106893200	Enhancers	Placenta	Placenta
16	chr5:106890400-106893400	Enhancers	Osteobl	bone
17	chr5:106890400-106893600	Enhancers	NH-A	brain
18	chr5:106890400-106893800	Enhancers	NHDF-Ad	bronchial
19	chr5:106890400-106894000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:106890400-106894800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:106890400-106895000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:106890600-106893400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:106891000-106899800	Weak transcription	Aorta	Aorta
24	chr5:106891200-106893800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr5:106891200-106893800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:106891400-106893200	Weak transcription	Fetal Kidney	kidney
27	chr5:106891400-106895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:106891400-106895000	Enhancers	HMEC	breast
29	chr5:106892000-106901800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:106892200-106895600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:106892600-106893400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:106892600-106893400	Enhancers	Liver	Liver
33	chr5:106892600-106893400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:106892600-106893600	Flanking Active TSS	A549	lung
35	chr5:106892600-106893800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:106892600-106894000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr5:106892600-106894400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr5:106892600-106895000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr5:106892600-106895400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr5:106892600-106895400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr5:106892800-106893200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr5:106892800-106893200	Enhancers	Left Ventricle	heart
43	chr5:106892800-106893200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr5:106892800-106893200	Enhancers	GM12878-XiMat	blood
45	chr5:106892800-106893400	Enhancers	Stomach Mucosa	stomach
46	chr5:106892800-106893400	Enhancers	HSMMtube	muscle
47	chr5:106892800-106893600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:106892800-106893800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:106892800-106894800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:106892800-106895600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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