Variant report

Variant	rs12880360
Chromosome Location	chr14:64868019-64868020
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	chr14:64860062..64863204-chr14:64866083..64868815,3	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1256112	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12587229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12886138	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34110441	0.81[AMR][1000 genomes];0.89[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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12880360	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs12880360	SYNE2	cis	multi-tissue	Pritchard
rs12880360	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs12880360	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64856000-64869800	Weak transcription	Placenta	Placenta
2	chr14:64856000-64886200	Weak transcription	Fetal Brain Male	brain
3	chr14:64856000-64913000	Weak transcription	Small Intestine	intestine
4	chr14:64856200-64870400	Weak transcription	Fetal Brain Female	brain
5	chr14:64856200-64870400	Weak transcription	Fetal Intestine Large	intestine
6	chr14:64856200-64882200	Weak transcription	HSMMtube	muscle
7	chr14:64856200-64883800	Weak transcription	Esophagus	oesophagus
8	chr14:64856200-64885600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:64856200-64886400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:64856200-64931200	Weak transcription	Stomach Mucosa	stomach
11	chr14:64856400-64870400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr14:64856400-64870600	Weak transcription	Psoas Muscle	Psoas
13	chr14:64856400-64875800	Weak transcription	Thymus	Thymus
14	chr14:64856400-64877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr14:64856400-64882400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:64856600-64870600	Weak transcription	NH-A	brain
17	chr14:64856600-64879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr14:64856800-64868400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr14:64856800-64868400	Weak transcription	Osteobl	bone
20	chr14:64856800-64868600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:64856800-64868600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:64856800-64870400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr14:64856800-64870600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:64856800-64877800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:64856800-64881800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr14:64856800-64881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:64856800-64882000	Weak transcription	Fetal Lung	lung
28	chr14:64856800-64882000	Weak transcription	NHLF	lung
29	chr14:64856800-64885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr14:64857000-64868800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr14:64857000-64870600	Weak transcription	NHDF-Ad	bronchial
32	chr14:64857000-64881800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:64857200-64880400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr14:64858000-64870600	Weak transcription	Fetal Kidney	kidney
35	chr14:64858600-64868600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:64858600-64870600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr14:64858600-64872200	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:64858800-64869600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr14:64858800-64870400	Weak transcription	Primary B cells from cord blood	blood
40	chr14:64859000-64878000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:64859000-64879400	Weak transcription	Lung	lung
42	chr14:64859200-64869200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr14:64859400-64868600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr14:64859400-64868600	Weak transcription	HUVEC	blood vessel
45	chr14:64859400-64870400	Weak transcription	Fetal Thymus	thymus
46	chr14:64859400-64870600	Weak transcription	Brain Anterior Caudate	brain
47	chr14:64859400-64875400	Weak transcription	Aorta	Aorta
48	chr14:64859400-64877000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:64859600-64868600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr14:64860600-64877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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