Variant report

Variant	rs1523519
Chromosome Location	chr3:121631841-121631842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121552625..121554974-chr3:121631455..121633032,2	MCF-7	breast:
2	chr3:121630605..121632622-chr3:121633802..121636620,2	MCF-7	breast:
3	chr3:121630868..121633208-chr3:121798735..121801092,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173226	Chromatin interaction
ENSG00000145088	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10934565	0.86[AMR][1000 genomes]
rs12488334	0.84[AMR][1000 genomes]
rs12488851	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs12489233	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491991	0.84[AMR][1000 genomes]
rs12493408	0.84[AMR][1000 genomes]
rs12493952	0.83[AMR][1000 genomes]
rs12496036	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497349	0.83[AMR][1000 genomes]
rs12630486	0.83[AMR][1000 genomes]
rs12637351	0.84[AMR][1000 genomes]
rs13067270	0.86[AMR][1000 genomes]
rs13083557	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs13089878	0.84[AMR][1000 genomes]
rs1920290	0.86[AMR][1000 genomes]
rs1920291	0.85[AMR][1000 genomes]
rs1920299	0.86[MEX][hapmap]
rs1920309	0.86[AMR][1000 genomes]
rs1986368	0.84[AMR][1000 genomes]
rs1986712	0.83[AMR][1000 genomes]
rs2091664	0.84[AMR][1000 genomes]
rs2293611	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332033	0.85[AMR][1000 genomes]
rs2689290	0.86[MEX][hapmap]
rs2877560	0.84[AMR][1000 genomes]
rs28823352	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34158925	0.82[AMR][1000 genomes]
rs34181646	0.83[AMR][1000 genomes]
rs34478505	0.84[AMR][1000 genomes]
rs34543553	0.84[AMR][1000 genomes]
rs34566912	0.85[AMR][1000 genomes]
rs34696871	0.85[AMR][1000 genomes]
rs34837785	0.87[AMR][1000 genomes]
rs35101693	0.86[AMR][1000 genomes]
rs35415993	0.86[AMR][1000 genomes]
rs35737776	0.84[AMR][1000 genomes]
rs35902163	0.87[AMR][1000 genomes]
rs3942629	0.91[MEX][hapmap]
rs4118376	0.87[AMR][1000 genomes]
rs4285028	0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs4305455	0.86[AMR][1000 genomes]
rs6790281	0.87[AMR][1000 genomes]
rs71329246	0.84[AMR][1000 genomes]
rs71329247	0.85[AMR][1000 genomes]
rs73855476	0.89[AMR][1000 genomes]
rs73855480	0.84[AMR][1000 genomes]
rs73855481	0.84[AMR][1000 genomes]
rs7615571	0.86[AMR][1000 genomes]
rs7637495	0.86[MEX][hapmap]
rs7640872	0.84[AMR][1000 genomes]
rs7651226	0.86[AMR][1000 genomes]

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	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1523519	GOLGB1	cis	multi-tissue	Pritchard
rs1523519	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs1523519	IQCB1	cis	cerebellum	SCAN
rs1523519	FAM162A	cis	cerebellum	SCAN
rs1523519	EAF2	cis	cerebellum	SCAN
rs1523519	IQCB1	cis	Esophagus Muscularis	GTEx
rs1523519	IQCB1	cis	parietal	SCAN
rs1523519	SLC15A2	cis	parietal	SCAN
rs1523519	SLC15A2	cis	cerebellum	SCAN
rs1523519	HEG1	cis	cerebellum	SCAN
rs1523519	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs1523519	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121592800-121646800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:121593000-121632400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:121613800-121647200	Weak transcription	Left Ventricle	heart
4	chr3:121614000-121632800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:121614000-121633200	Weak transcription	Fetal Kidney	kidney
6	chr3:121614000-121637800	Weak transcription	Spleen	Spleen
7	chr3:121614200-121634400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:121615000-121632000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:121615600-121633200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
11	chr3:121616200-121637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:121616200-121659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:121623400-121639200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:121624000-121647800	Weak transcription	Adipose Nuclei	Adipose
15	chr3:121625000-121661200	Weak transcription	Thymus	Thymus
16	chr3:121625200-121640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:121626200-121651600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:121626800-121638600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:121627200-121632000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:121627200-121632400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:121627200-121635800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:121627400-121634400	Weak transcription	Primary T cells from cord blood	blood
23	chr3:121627400-121641600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:121627400-121659200	Weak transcription	Lung	lung
25	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
26	chr3:121627600-121633200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:121627600-121645200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:121627600-121659200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:121627800-121633800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:121627800-121635400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:121628200-121638200	Strong transcription	GM12878-XiMat	blood
32	chr3:121628200-121659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:121628400-121637200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:121629800-121651400	Strong transcription	Primary B cells from cord blood	blood
35	chr3:121630200-121652200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:121630400-121649600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:121631600-121632000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:121631600-121632000	Enhancers	Brain Anterior Caudate	brain
39	chr3:121631600-121632200	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:121631600-121633600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:121631800-121632800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain

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