Variant report

Variant	rs2867878
Chromosome Location	chr18:13370324-13370325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13361048..13363977-chr18:13367338..13370416,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1107340	0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1225	1.00[ASW][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs12458775	1.00[YRI][hapmap]
rs12608402	0.94[EUR][1000 genomes]
rs12960927	0.80[AMR][1000 genomes]
rs12962774	1.00[YRI][hapmap]
rs1551367	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17681051	1.00[YRI][hapmap]
rs1893975	0.88[EUR][1000 genomes]
rs2085049	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.85[AMR][1000 genomes]
rs2276392	0.83[MEX][hapmap]
rs2867877	0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35815061	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3960634	0.88[AMR][1000 genomes]
rs4797760	0.83[AMR][1000 genomes]
rs4797761	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.83[AMR][1000 genomes]
rs4797764	1.00[ASW][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs4797765	0.82[AMR][1000 genomes]
rs6505810	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7230215	0.93[EUR][1000 genomes]
rs7244756	0.93[EUR][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2867878	C18orf19	cis	cerebellum	SCAN
rs2867878	BAZ1A	trans	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

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	chr18:13362000-13374600	Weak transcription	Fetal Muscle Leg	muscle
9	chr18:13364200-13371400	Enhancers	Fetal Thymus	thymus
10	chr18:13365200-13372200	Weak transcription	Brain Angular Gyrus	brain
11	chr18:13365800-13371200	Weak transcription	Fetal Brain Female	brain
12	chr18:13365800-13376400	Weak transcription	Liver	Liver
13	chr18:13366800-13374200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr18:13367200-13372200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:13367200-13372200	Weak transcription	Brain Substantia Nigra	brain
16	chr18:13367200-13374600	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:13367800-13371200	Weak transcription	Spleen	Spleen
18	chr18:13367800-13371800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr18:13367800-13372600	Weak transcription	Lung	lung
20	chr18:13367800-13374800	Weak transcription	Right Atrium	heart
21	chr18:13368200-13372000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr18:13368600-13371400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr18:13368800-13370600	Enhancers	Right Ventricle	heart
24	chr18:13368800-13372200	Weak transcription	Brain Anterior Caudate	brain
25	chr18:13369000-13370400	Enhancers	Fetal Intestine Small	intestine
26	chr18:13369000-13370400	Enhancers	Stomach Smooth Muscle	stomach
27	chr18:13369000-13370600	Enhancers	Colon Smooth Muscle	Colon
28	chr18:13369000-13370600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr18:13369000-13373600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr18:13369200-13370400	Enhancers	Colonic Mucosa	Colon
31	chr18:13369200-13370600	Enhancers	Fetal Intestine Large	intestine
32	chr18:13369200-13370800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr18:13369200-13370800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr18:13369200-13373000	Enhancers	Primary T cells fromperipheralblood	blood
35	chr18:13369200-13374600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr18:13369400-13370400	Enhancers	Fetal Stomach	stomach
37	chr18:13369400-13370600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr18:13369400-13370600	Enhancers	Primary T cells from cord blood	blood
39	chr18:13369400-13370600	Enhancers	Stomach Mucosa	stomach
40	chr18:13369400-13372000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:13369600-13370400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr18:13369600-13370600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr18:13369600-13370600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr18:13369600-13370600	Enhancers	NH-A	brain
45	chr18:13369600-13371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr18:13369600-13374600	Weak transcription	Gastric	stomach
47	chr18:13369800-13370400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:13369800-13370400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr18:13369800-13370400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr18:13369800-13370800	Enhancers	Small Intestine	intestine

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