Variant report

Variant	rs12456874
Chromosome Location	chr18:13366862-13366863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13366355..13367895-chr18:13449002..13451702,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11659711	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11659822	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11661280	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11663785	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11665476	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12456859	0.92[EUR][1000 genomes]
rs12955917	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1454128	0.92[EUR][1000 genomes]
rs1573507	1.00[LWK][hapmap]
rs16940349	0.90[CEU][hapmap]
rs1840267	0.81[EUR][1000 genomes]
rs1869497	0.90[CEU][hapmap]
rs1893980	0.83[CEU][hapmap]
rs2085050	0.88[CEU][hapmap]
rs2187502	0.90[CEU][hapmap]
rs2276392	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs2867874	0.89[CEU][hapmap]
rs4570935	0.89[CEU][hapmap]
rs55882226	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7226901	0.89[CEU][hapmap]
rs7227361	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7234501	0.85[CEU][hapmap]
rs7236152	0.89[CEU][hapmap]
rs7241109	0.90[CEU][hapmap]
rs7241410	0.90[CEU][hapmap]
rs7241438	0.90[CEU][hapmap]
rs8087505	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs8088874	0.82[EUR][1000 genomes]
rs8092304	0.87[EUR][1000 genomes]
rs8094197	0.90[CEU][hapmap]
rs897035	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs930797	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs930798	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs930799	0.85[CEU][hapmap]
rs949259	0.90[CEU][hapmap]
rs9952836	1.00[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9954359	0.90[CEU][hapmap]
rs9957335	0.92[EUR][1000 genomes]
rs9957621	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs9960893	0.85[EUR][1000 genomes]
rs9963572	0.94[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Pancreatic cancer	23180869	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12456874	XPO6	trans	lymphoblastoid	seeQTL
rs12456874	TUBB6	cis	cerebellum	SCAN
rs12456874	AFG3L2	cis	cerebellum	SCAN
rs12456874	C18orf19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13351800-13374800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr18:13354200-13371800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr18:13354200-13372000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:13354400-13371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr18:13355000-13374200	Weak transcription	Dnd41	blood
6	chr18:13356400-13379200	Weak transcription	Aorta	Aorta
7	chr18:13359400-13379400	Weak transcription	Psoas Muscle	Psoas
8	chr18:13361600-13369400	Weak transcription	Pancreas	Pancrea
9	chr18:13362000-13367200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr18:13362000-13374600	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:13363200-13367200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr18:13363200-13369800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr18:13363600-13369200	Weak transcription	Fetal Heart	heart
14	chr18:13364200-13371400	Enhancers	Fetal Thymus	thymus
15	chr18:13365000-13369000	Weak transcription	HepG2	liver
16	chr18:13365200-13367000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr18:13365200-13367000	Weak transcription	Left Ventricle	heart
18	chr18:13365200-13367400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr18:13365200-13367400	Weak transcription	Right Atrium	heart
20	chr18:13365200-13367600	Weak transcription	Spleen	Spleen
21	chr18:13365200-13368800	Enhancers	Brain Anterior Caudate	brain
22	chr18:13365200-13369400	Weak transcription	Primary T cells from cord blood	blood
23	chr18:13365200-13372200	Weak transcription	Brain Angular Gyrus	brain
24	chr18:13365400-13367000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr18:13365400-13368800	Weak transcription	Right Ventricle	heart
26	chr18:13365600-13367000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr18:13365600-13367000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:13365600-13369200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr18:13365600-13369200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr18:13365600-13369600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr18:13365800-13369000	Weak transcription	Colon Smooth Muscle	Colon
32	chr18:13365800-13369000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr18:13365800-13370000	Weak transcription	Fetal Brain Male	brain
34	chr18:13365800-13371200	Weak transcription	Fetal Brain Female	brain
35	chr18:13365800-13376400	Weak transcription	Liver	Liver
36	chr18:13366000-13367200	Enhancers	Brain Hippocampus Middle	brain
37	chr18:13366200-13367400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr18:13366400-13367000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr18:13366600-13367200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr18:13366600-13367200	Enhancers	Fetal Muscle Trunk	muscle
41	chr18:13366600-13367800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr18:13366800-13367000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr18:13366800-13367200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr18:13366800-13367200	Enhancers	Brain Cingulate Gyrus	brain
45	chr18:13366800-13367200	Enhancers	Brain Substantia Nigra	brain
46	chr18:13366800-13367200	Enhancers	Thymus	Thymus
47	chr18:13366800-13367800	Enhancers	Brain Germinal Matrix	brain
48	chr18:13366800-13368600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr18:13366800-13369400	Weak transcription	Gastric	stomach
50	chr18:13366800-13374200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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