Variant report

Variant	rs11564412
Chromosome Location	chr18:25619000-25619001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:25618996-25619349	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CDH2	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10502506	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs10502507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1078501	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10853680	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083245	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11083246	0.88[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes]
rs11083248	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs1122356	0.82[CHB][hapmap]
rs11564297	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11564308	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564316	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11564329	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs11564330	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11564332	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11564393	0.93[CHB][hapmap];0.86[EUR][1000 genomes]
rs11564397	0.87[CEU][hapmap];0.86[CHB][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs11564405	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11564409	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11564413	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11873053	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12958882	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373136	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1443450	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443451	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443453	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17445875	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17446001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462962	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17463213	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs17463233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes]
rs17463295	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs17468531	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs17468636	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs17468678	0.93[CEU][hapmap];0.94[CHB][hapmap]
rs1808940	0.87[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes]
rs1816825	0.82[CHB][hapmap]
rs1838161	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1941180	0.94[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1944292	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[EUR][1000 genomes]
rs1944294	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1972934	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2053599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs2156605	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218361	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2310784	0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144654	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4598992	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4800837	0.88[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs4800838	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4800839	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4800840	0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs4800841	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs490820	0.83[CHB][hapmap];0.89[AMR][1000 genomes]
rs500643	0.82[CHB][hapmap]
rs533602	0.81[AMR][1000 genomes]
rs539075	0.81[CHB][hapmap]
rs565509	0.83[CHB][hapmap]
rs568575	0.88[AMR][1000 genomes]
rs576467	0.83[CHB][hapmap]
rs597591	0.82[CHB][hapmap]
rs614966	0.82[CHB][hapmap]
rs623234	0.82[CHB][hapmap]
rs647733	0.83[CHB][hapmap]
rs656642	0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs665781	0.82[CHB][hapmap]
rs673008	0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs694943	0.83[CHB][hapmap]
rs7230771	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs72639459	0.90[EUR][1000 genomes]
rs8091763	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8092004	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874314	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs894679	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs9635986	0.81[EUR][1000 genomes]
rs9789154	0.83[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs9789221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.85[ASN][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	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833605	chr18:25467096-25643447	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25583800-25621400	Weak transcription	Right Ventricle	heart
2	chr18:25600000-25619000	Weak transcription	HSMM	muscle
3	chr18:25609800-25621600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:25612400-25619000	Weak transcription	Brain Germinal Matrix	brain
5	chr18:25612800-25619000	Weak transcription	A549	lung
6	chr18:25615200-25624600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:25616800-25625000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr18:25617000-25619200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr18:25617000-25619400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr18:25617000-25620000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:25617000-25620400	Weak transcription	Osteobl	bone
12	chr18:25617000-25625000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr18:25617000-25628800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr18:25617200-25619800	Weak transcription	Brain Hippocampus Middle	brain
15	chr18:25617200-25621200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr18:25617400-25619000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr18:25617400-25619800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr18:25617400-25620200	Weak transcription	Brain Angular Gyrus	brain
19	chr18:25617400-25625000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:25617400-25625200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr18:25617600-25619000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:25617600-25619000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr18:25617600-25619000	Weak transcription	Liver	Liver
24	chr18:25617600-25619000	Weak transcription	Brain Anterior Caudate	brain
25	chr18:25617600-25619800	Weak transcription	Brain Substantia Nigra	brain
26	chr18:25617800-25619000	Weak transcription	NH-A	brain
27	chr18:25617800-25619600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr18:25617800-25621400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:25618000-25619000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr18:25618000-25619600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr18:25618000-25624200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr18:25618000-25624200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:25618200-25619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:25618200-25620000	Weak transcription	Fetal Brain Female	brain
35	chr18:25618200-25620400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:25618200-25620600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:25618400-25619200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:25618400-25619200	Weak transcription	Left Ventricle	heart
39	chr18:25618400-25631600	Weak transcription	Fetal Brain Male	brain
40	chr18:25618600-25620400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr18:25618800-25619800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr18:25618800-25620200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:25618800-25620600	Enhancers	HUVEC	blood vessel
44	chr18:25618800-25622000	Enhancers	Fetal Heart	heart
45	chr18:25619000-25619200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr18:25619000-25619200	Enhancers	Brain Anterior Caudate	brain
47	chr18:25619000-25619400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr18:25619000-25619400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr18:25619000-25619400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr18:25619000-25619600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links