Variant report

Variant	rs12880777
Chromosome Location	chr14:70874695-70874696
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	chr14:70824855..70826535-chr14:70873989..70876965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133983	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1060681	0.82[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11158858	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11626228	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626414	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628785	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12433609	0.86[AFR][1000 genomes]
rs12590808	0.90[ASN][1000 genomes]
rs12880929	0.86[AFR][1000 genomes]
rs12884918	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12893988	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17475516	0.82[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17476399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17567627	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1953800	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2022624	0.85[AMR][1000 genomes]
rs2877661	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34273029	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34511042	0.90[ASN][1000 genomes]
rs34767236	0.86[ASN][1000 genomes]
rs34866539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764183	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7493545	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8016418	0.82[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs8019852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][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	nsv902075	chr14:70612618-70919016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12880777	C14orf162	cis	cerebellum	SCAN
rs12880777	SMOC1	cis	cerebellum	SCAN
rs12880777	ADAM20	cis	cerebellum	SCAN
rs12880777	PAPLN	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70827200-70882600	Weak transcription	A549	lung
2	chr14:70827200-70882600	Weak transcription	NH-A	brain
3	chr14:70833800-70882400	Weak transcription	NHDF-Ad	bronchial
4	chr14:70838600-70882400	Weak transcription	Hela-S3	cervix
5	chr14:70840200-70882400	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:70840200-70882600	Weak transcription	Colonic Mucosa	Colon
7	chr14:70840800-70882800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:70841000-70882600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr14:70841400-70879800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr14:70842600-70882400	Weak transcription	Fetal Kidney	kidney
11	chr14:70846800-70878600	Weak transcription	HSMM	muscle
12	chr14:70848400-70882400	Weak transcription	Brain Angular Gyrus	brain
13	chr14:70848400-70882800	Weak transcription	Psoas Muscle	Psoas
14	chr14:70848400-70883000	Weak transcription	HSMMtube	muscle
15	chr14:70848600-70882400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:70848600-70882800	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:70848800-70882600	Weak transcription	Brain Substantia Nigra	brain
18	chr14:70853600-70882400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:70853800-70880800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:70854800-70882400	Weak transcription	Brain Anterior Caudate	brain
21	chr14:70855000-70875400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:70855200-70882400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:70855600-70875600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:70856000-70882400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr14:70859000-70882800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:70864600-70880000	Weak transcription	Esophagus	oesophagus
27	chr14:70864800-70875600	Weak transcription	Liver	Liver
28	chr14:70864800-70875600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr14:70864800-70875800	Weak transcription	Placenta	Placenta
30	chr14:70864800-70877200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr14:70865000-70876000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr14:70865000-70878400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr14:70865000-70882400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr14:70865000-70882800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:70865200-70882800	Weak transcription	Aorta	Aorta
36	chr14:70865400-70875600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr14:70865400-70875600	Weak transcription	Fetal Lung	lung
38	chr14:70865400-70877400	Weak transcription	Primary B cells from cord blood	blood
39	chr14:70865400-70882600	Weak transcription	Brain Hippocampus Middle	brain
40	chr14:70865600-70880200	Weak transcription	HepG2	liver
41	chr14:70865800-70875400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:70865800-70882600	Weak transcription	Adipose Nuclei	Adipose
43	chr14:70866000-70882600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr14:70866200-70875400	Weak transcription	Fetal Intestine Large	intestine
45	chr14:70866200-70878200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr14:70866400-70875400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr14:70866400-70875600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:70866400-70875600	Weak transcription	Fetal Stomach	stomach
49	chr14:70866400-70876200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr14:70866400-70881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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