Variant report

Variant	rs12434608
Chromosome Location	chr14:64859293-64859294
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:64852898..64856787-chr14:64858975..64865298,10	K562	blood:
2	chr14:64853586..64859592-chr14:64968792..64973445,7	MCF-7	breast:
3	chr14:64857964..64859917-chr14:64874810..64877403,2	MCF-7	breast:
4	chr14:64852868..64856787-chr14:64858237..64862286,8	K562	blood:
5	chr14:64857748..64860531-chr14:64970254..64972239,2	K562	blood:
6	chr14:64802845..64807201-chr14:64857442..64860661,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140009	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11158538	0.82[EUR][1000 genomes]
rs1256093	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1256095	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256097	0.88[EUR][1000 genomes]
rs1256099	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1256100	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256101	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256102	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256107	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256108	0.89[EUR][1000 genomes]
rs1256109	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256111	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1256113	0.81[EUR][1000 genomes]
rs1262246	0.89[EUR][1000 genomes]
rs1270057	0.90[EUR][1000 genomes]
rs12889097	0.93[EUR][1000 genomes]
rs12894546	0.97[EUR][1000 genomes]
rs2983741	0.81[EUR][1000 genomes]
rs2983742	0.82[EUR][1000 genomes]
rs35020344	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs36016358	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4243628	0.94[EUR][1000 genomes]
rs57087457	0.83[EUR][1000 genomes]
rs7151163	0.81[EUR][1000 genomes]
rs8010584	0.80[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12434608	MTHFD1	cis	Thyroid	GTEx
rs12434608	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs12434608	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12434608	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs12434608	SYNE2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 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	chr14:64856200-64860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:64856200-64860200	Weak transcription	Ovary	ovary
6	chr14:64856200-64860200	Weak transcription	Right Ventricle	heart
7	chr14:64856200-64860400	Weak transcription	Spleen	Spleen
8	chr14:64856200-64861200	Weak transcription	Brain Substantia Nigra	brain
9	chr14:64856200-64867200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:64856200-64870400	Weak transcription	Fetal Brain Female	brain
11	chr14:64856200-64870400	Weak transcription	Fetal Intestine Large	intestine
12	chr14:64856200-64882200	Weak transcription	HSMMtube	muscle
13	chr14:64856200-64883800	Weak transcription	Esophagus	oesophagus
14	chr14:64856200-64885600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:64856200-64886400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr14:64856200-64931200	Weak transcription	Stomach Mucosa	stomach
17	chr14:64856400-64860200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:64856400-64860200	Weak transcription	Gastric	stomach
19	chr14:64856400-64861400	Weak transcription	Colonic Mucosa	Colon
20	chr14:64856400-64870400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr14:64856400-64870600	Weak transcription	Psoas Muscle	Psoas
22	chr14:64856400-64875800	Weak transcription	Thymus	Thymus
23	chr14:64856400-64877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:64856400-64882400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr14:64856600-64859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr14:64856600-64860200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr14:64856600-64861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr14:64856600-64867600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr14:64856600-64870600	Weak transcription	NH-A	brain
30	chr14:64856600-64879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:64856800-64860200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr14:64856800-64860200	Weak transcription	Fetal Heart	heart
33	chr14:64856800-64862800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:64856800-64867200	Weak transcription	Brain Germinal Matrix	brain
35	chr14:64856800-64867400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:64856800-64868400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr14:64856800-64868400	Weak transcription	Osteobl	bone
38	chr14:64856800-64868600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr14:64856800-64868600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr14:64856800-64870400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:64856800-64870600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:64856800-64877800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr14:64856800-64881800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr14:64856800-64881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr14:64856800-64882000	Weak transcription	Fetal Lung	lung
46	chr14:64856800-64882000	Weak transcription	NHLF	lung
47	chr14:64856800-64885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:64857000-64860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:64857000-64860400	Weak transcription	Primary T cells from cord blood	blood
50	chr14:64857000-64862800	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links