Variant report

Variant	rs12925371
Chromosome Location	chr16:69773885-69773886
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	chr16:69755773..69764501-chr16:69767489..69780977,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000262136	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10048108	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10163235	0.88[EUR][1000 genomes]
rs10454066	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10500551	0.82[EUR][1000 genomes]
rs11075733	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075734	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1139178	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11639947	0.82[EUR][1000 genomes]
rs11641233	0.82[EUR][1000 genomes]
rs11641521	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11643926	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11644838	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11644914	0.90[EUR][1000 genomes]
rs11646884	0.83[EUR][1000 genomes]
rs12232410	0.85[EUR][1000 genomes]
rs12446201	0.87[EUR][1000 genomes]
rs12447883	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12595869	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12596679	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1437135	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1437136	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16959025	0.82[EUR][1000 genomes]
rs16959035	0.87[EUR][1000 genomes]
rs1800566	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1865965	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2118220	0.82[EUR][1000 genomes]
rs2196574	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2217950	0.82[EUR][1000 genomes]
rs2361838	0.82[EUR][1000 genomes]
rs2361839	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3169315	0.82[EUR][1000 genomes]
rs3743673	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3811349	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078387	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4464069	0.91[EUR][1000 genomes]
rs4497676	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4580150	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4985518	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985523	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55701476	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55863174	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55992518	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56282083	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56316408	0.83[EUR][1000 genomes]
rs57488237	0.87[EUR][1000 genomes]
rs57518557	0.90[EUR][1000 genomes]
rs57565297	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59295369	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60010276	0.81[EUR][1000 genomes]
rs60231938	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60472033	0.83[EUR][1000 genomes]
rs61426398	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499253	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499255	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs689455	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7186002	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7189424	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7198242	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73579458	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73579497	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74029403	0.85[EUR][1000 genomes]
rs8045142	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8045682	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8046314	0.85[EUR][1000 genomes]
rs8047885	0.83[EUR][1000 genomes]
rs8052086	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8053080	0.82[EUR][1000 genomes]
rs8054096	0.85[EUR][1000 genomes]
rs8059345	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8060588	0.83[EUR][1000 genomes]
rs9788837	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9921045	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9933526	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12925371	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69761200-69775400	Weak transcription	Fetal Brain Male	brain
2	chr16:69761200-69776200	Weak transcription	Ovary	ovary
3	chr16:69761400-69774200	Weak transcription	Esophagus	oesophagus
4	chr16:69761400-69774200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr16:69761600-69774000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr16:69761600-69774000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:69761600-69774000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr16:69761600-69774200	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:69761600-69774200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr16:69761800-69774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:69761800-69774200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr16:69761800-69774200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr16:69761800-69774200	Weak transcription	Brain Substantia Nigra	brain
14	chr16:69761800-69774200	Weak transcription	NHEK	skin
15	chr16:69761800-69774200	Weak transcription	NHLF	lung
16	chr16:69761800-69774400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:69761800-69787400	Weak transcription	Right Atrium	heart
18	chr16:69762000-69774000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr16:69762000-69774000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr16:69762000-69774200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr16:69762200-69774000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:69762200-69776400	Weak transcription	Small Intestine	intestine
23	chr16:69762400-69775200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:69762800-69774200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:69762800-69774200	Weak transcription	Brain Angular Gyrus	brain
26	chr16:69762800-69774200	Weak transcription	Brain Hippocampus Middle	brain
27	chr16:69762800-69774200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr16:69762800-69774400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr16:69762800-69775000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr16:69766000-69776400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr16:69766600-69775400	Weak transcription	Stomach Mucosa	stomach
32	chr16:69766800-69774200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr16:69766800-69774200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr16:69767400-69774000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:69767800-69774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr16:69767800-69775200	Weak transcription	NHDF-Ad	bronchial
37	chr16:69768000-69774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr16:69768600-69774200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:69769600-69774200	Weak transcription	Fetal Kidney	kidney
40	chr16:69769800-69775000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr16:69770200-69778600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr16:69770400-69777400	Weak transcription	Right Ventricle	heart
43	chr16:69770400-69788000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr16:69770600-69775600	Weak transcription	Fetal Heart	heart
45	chr16:69770800-69775200	Weak transcription	Colonic Mucosa	Colon
46	chr16:69771000-69774400	Weak transcription	Brain Anterior Caudate	brain
47	chr16:69771200-69775200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr16:69771600-69774400	Weak transcription	Aorta	Aorta
49	chr16:69771600-69775200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr16:69771600-69775200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links