Variant report

Variant	rs354288
Chromosome Location	chr5:14237265-14237266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14235633..14238119-chr5:14245399..14248312,2	MCF-7	breast:
2	chr5:14216973..14219606-chr5:14236627..14239606,2	MCF-7	breast:
3	chr5:14149488..14151474-chr5:14236779..14238294,2	MCF-7	breast:
4	chr5:14228783..14230881-chr5:14236364..14239220,3	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CHB][hapmap]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs151901	1.00[ASN][1000 genomes]
rs151902	1.00[ASN][1000 genomes]
rs164858	1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs17299506	1.00[ASN][1000 genomes]
rs17302408	1.00[CHB][hapmap]
rs187125	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs187386	1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap]
rs245447	1.00[ASN][1000 genomes]
rs245448	1.00[ASN][1000 genomes]
rs245470	1.00[ASN][1000 genomes]
rs245512	1.00[ASN][1000 genomes]
rs26057	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs26058	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs26059	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs26060	1.00[ASN][1000 genomes]
rs26061	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs27759	1.00[ASN][1000 genomes]
rs28010	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs30616	1.00[CHB][hapmap]
rs30617	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs30619	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs30620	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs32335	1.00[ASN][1000 genomes]
rs32339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs32341	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs32388	1.00[ASN][1000 genomes]
rs32389	1.00[ASN][1000 genomes]
rs32390	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs32391	1.00[ASN][1000 genomes]
rs32394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs32395	1.00[ASN][1000 genomes]
rs354285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354287	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs354298	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs354299	1.00[ASN][1000 genomes]
rs354300	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs354301	1.00[ASN][1000 genomes]
rs354305	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs354308	0.81[AMR][1000 genomes]
rs354310	1.00[ASN][1000 genomes]
rs354311	1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs35594035	1.00[ASN][1000 genomes]
rs3849082	1.00[CHB][hapmap]
rs397098	1.00[ASN][1000 genomes]
rs39856	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs407517	1.00[ASN][1000 genomes]
rs424275	0.83[ASN][1000 genomes]
rs445553	1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs533517	1.00[ASN][1000 genomes]
rs56235530	1.00[ASN][1000 genomes]
rs706271	0.83[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap]
rs773701	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs773702	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs773703	1.00[CHB][hapmap]
rs773763	1.00[CHB][hapmap]
rs923616	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	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv4724	chr5:14225543-14243167	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs354288	TOX	trans	lymphoblastoid	seeQTL
rs354288	MYO10	cis	parietal	SCAN
rs354288	INSC	trans	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14221800-14249600	Weak transcription	Colonic Mucosa	Colon
2	chr5:14223800-14237600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:14224000-14237400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:14224000-14239600	Weak transcription	Primary B cells from cord blood	blood
5	chr5:14225000-14237600	Genic enhancers	HSMM	muscle
6	chr5:14226200-14237800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:14226400-14249400	Weak transcription	Esophagus	oesophagus
8	chr5:14226600-14246800	Weak transcription	Fetal Intestine Small	intestine
9	chr5:14227000-14237400	Weak transcription	Spleen	Spleen
10	chr5:14227200-14237400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:14227400-14237400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:14227600-14239000	Weak transcription	Gastric	stomach
13	chr5:14228600-14237400	Weak transcription	Hela-S3	cervix
14	chr5:14229000-14237600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr5:14230000-14237600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:14230600-14237600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:14230800-14238400	Weak transcription	Fetal Brain Female	brain
18	chr5:14231400-14239800	Weak transcription	Small Intestine	intestine
19	chr5:14231600-14237800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:14231800-14238600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:14232000-14238000	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:14232200-14240600	Weak transcription	Fetal Intestine Large	intestine
23	chr5:14233200-14237600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:14233800-14237400	Enhancers	A549	lung
25	chr5:14234200-14240000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:14234400-14237600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr5:14234600-14237400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:14234600-14237400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:14234600-14237400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:14234600-14237400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:14234600-14237400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:14234600-14237400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:14234600-14237400	Weak transcription	Ovary	ovary
34	chr5:14234600-14237400	Weak transcription	Right Ventricle	heart
35	chr5:14234600-14237400	Weak transcription	NHDF-Ad	bronchial
36	chr5:14234600-14237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:14234600-14242600	Weak transcription	Lung	lung
38	chr5:14234600-14250200	Weak transcription	Placenta	Placenta
39	chr5:14234800-14237400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:14234800-14237400	Weak transcription	NHEK	skin
41	chr5:14235600-14240000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:14235800-14237400	Weak transcription	HMEC	breast
43	chr5:14235800-14237400	Weak transcription	Osteobl	bone
44	chr5:14236000-14237400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:14236200-14237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:14236200-14237400	Weak transcription	NHLF	lung
47	chr5:14236200-14239200	Enhancers	HUVEC	blood vessel
48	chr5:14236400-14240800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr5:14236400-14240800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr5:14236400-14240800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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