Variant report

Variant	rs12590679
Chromosome Location	chr14:70813286-70813287
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	chr14:70812611..70814988-chr14:70825041..70827790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222640	Chromatin interaction
ENSG00000133983	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1044527	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11158855	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11623974	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11626325	0.90[ASN][1000 genomes]
rs12146968	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12147722	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12147825	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12433355	0.96[ASN][1000 genomes]
rs12588244	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589335	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12879801	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12887715	0.90[ASN][1000 genomes]
rs12890415	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2332372	0.86[ASN][1000 genomes]
rs2332373	0.85[ASN][1000 genomes]
rs2332421	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34802428	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35164282	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35186208	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35469188	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35671518	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35859016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759774	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61977537	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61977542	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61977552	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7141407	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7143274	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7144424	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7152898	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8005362	0.83[ASN][1000 genomes]
rs8014520	0.89[ASN][1000 genomes]
rs8015005	0.87[ASN][1000 genomes]
rs8015988	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8016060	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8021180	0.84[AMR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12590679	C14orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70788200-70813600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:70792800-70825200	Weak transcription	NH-A	brain
3	chr14:70798000-70817200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:70800000-70825000	Weak transcription	HSMM	muscle
5	chr14:70800600-70821000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr14:70800800-70815000	Weak transcription	Right Ventricle	heart
7	chr14:70800800-70824800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:70801200-70815200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:70801200-70815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:70801200-70822000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr14:70801200-70824200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr14:70801200-70825200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:70801800-70824400	Weak transcription	NHDF-Ad	bronchial
14	chr14:70802000-70824800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr14:70802000-70824800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr14:70802200-70813400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:70802200-70815200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr14:70802200-70822200	Weak transcription	NHEK	skin
19	chr14:70802400-70824800	Weak transcription	Brain Anterior Caudate	brain
20	chr14:70802600-70824800	Weak transcription	Brain Substantia Nigra	brain
21	chr14:70805000-70819000	ZNF genes & repeats	GM12878-XiMat	blood
22	chr14:70805000-70825200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr14:70806400-70823600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr14:70806600-70813400	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:70806600-70825200	Weak transcription	Fetal Kidney	kidney
26	chr14:70806800-70821200	Weak transcription	Aorta	Aorta
27	chr14:70806800-70825600	Weak transcription	Small Intestine	intestine
28	chr14:70807000-70821000	Weak transcription	Gastric	stomach
29	chr14:70807200-70822400	Weak transcription	Psoas Muscle	Psoas
30	chr14:70807400-70821400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr14:70807600-70821400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr14:70807800-70825200	Weak transcription	A549	lung
33	chr14:70808200-70817400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr14:70808600-70821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:70808600-70821800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr14:70809000-70821200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr14:70809400-70813400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:70809800-70821200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr14:70810000-70813600	ZNF genes & repeats	Fetal Brain Female	brain
40	chr14:70810200-70814000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr14:70810600-70813600	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr14:70810600-70814200	ZNF genes & repeats	Fetal Intestine Large	intestine
43	chr14:70810600-70816000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr14:70810600-70817200	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr14:70810600-70817400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr14:70810800-70821400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr14:70811200-70813400	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr14:70811200-70815800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
49	chr14:70811400-70814000	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr14:70811400-70824400	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links