Variant report

Variant	rs12885842
Chromosome Location	chr14:65918652-65918653
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	chr14:65906469..65908024-chr14:65917228..65919311,2	MCF-7	breast:
2	chr14:65912946..65915806-chr14:65916268..65918794,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10138671	0.84[CEU][hapmap]
rs10142283	0.96[CEU][hapmap]
rs10144979	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10145146	0.82[EUR][1000 genomes]
rs10150412	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10152007	0.93[CEU][hapmap]
rs10873190	0.81[AMR][1000 genomes]
rs10873191	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1113962	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11158595	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11158598	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11158603	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11158605	0.84[CEU][hapmap]
rs11158607	0.85[CEU][hapmap]
rs11623662	0.81[CEU][hapmap]
rs11629437	0.87[AMR][1000 genomes]
rs11844682	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12433597	0.93[CEU][hapmap]
rs12587057	0.92[CEU][hapmap]
rs1889731	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1953415	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1953418	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1959144	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs1959145	0.86[AMR][1000 genomes]
rs1999725	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2064695	0.81[CEU][hapmap]
rs2092914	0.88[CEU][hapmap]
rs2149839	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2183277	0.93[CEU][hapmap]
rs2184601	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2185454	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2210805	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2268956	0.92[CEU][hapmap]
rs2411356	0.81[CEU][hapmap]
rs2411815	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2411820	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2411823	0.85[CEU][hapmap]
rs2898814	0.96[CEU][hapmap]
rs2898818	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825639	0.92[CEU][hapmap]
rs4587890	0.84[CEU][hapmap]
rs4902399	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4902404	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6573612	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6573614	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6573615	0.80[CEU][hapmap]
rs6573616	0.92[CEU][hapmap]
rs7140341	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7140695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7141536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7142906	0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7143318	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144345	0.92[CEU][hapmap]
rs7144415	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7145500	0.96[CEU][hapmap];0.91[YRI][hapmap]
rs7145759	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs7146993	0.92[CEU][hapmap]
rs7147002	0.93[CEU][hapmap]
rs7147536	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7150094	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7150448	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7150648	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7151561	0.96[CEU][hapmap];0.87[AMR][1000 genomes]
rs7157109	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7158153	0.95[CEU][hapmap]
rs7160780	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs8003464	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8005243	0.80[ASN][1000 genomes]
rs8007497	0.93[CEU][hapmap]
rs8010726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8011224	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8012834	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8017880	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8019762	0.93[CEU][hapmap]
rs8022080	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9323460	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9323461	0.93[CEU][hapmap]
rs9972106	0.81[CEU][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65892800-65929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr14:65897000-65925600	Weak transcription	Aorta	Aorta
3	chr14:65898400-65935600	Weak transcription	Gastric	stomach
4	chr14:65899600-65929000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:65901200-65920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:65901800-65920200	Weak transcription	Brain Hippocampus Middle	brain
7	chr14:65902200-65927000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr14:65902400-65928400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr14:65903200-65922600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:65903200-65925200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:65905800-65936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:65906000-65923800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:65906000-65926800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr14:65906200-65919800	Weak transcription	Ovary	ovary
15	chr14:65906200-65922000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr14:65906600-65922800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:65907000-65920400	Weak transcription	K562	blood
18	chr14:65911200-65942400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:65912200-65922400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr14:65913000-65924000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr14:65913200-65920200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:65913200-65920400	Weak transcription	Fetal Lung	lung
23	chr14:65913200-65922400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:65913200-65927000	Weak transcription	NH-A	brain
25	chr14:65913200-65928000	Weak transcription	Osteobl	bone
26	chr14:65913600-65920400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr14:65913800-65920200	Weak transcription	Brain Angular Gyrus	brain
28	chr14:65913800-65920200	Weak transcription	Small Intestine	intestine
29	chr14:65913800-65922800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:65913800-65928000	Weak transcription	HUVEC	blood vessel
31	chr14:65913800-65942400	Weak transcription	Left Ventricle	heart
32	chr14:65914200-65922400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:65914600-65925000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:65915600-65928200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr14:65916000-65918800	ZNF genes & repeats	Dnd41	blood
36	chr14:65916000-65919400	ZNF genes & repeats	GM12878-XiMat	blood
37	chr14:65916400-65919000	Weak transcription	Brain Substantia Nigra	brain
38	chr14:65916600-65922600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr14:65916600-65923000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr14:65917200-65936600	Weak transcription	Pancreas	Pancrea
41	chr14:65917400-65918800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr14:65917400-65918800	ZNF genes & repeats	Fetal Thymus	thymus
43	chr14:65917600-65918800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr14:65917600-65918800	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr14:65917600-65918800	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr14:65917600-65918800	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr14:65917600-65918800	ZNF genes & repeats	Thymus	Thymus
48	chr14:65917800-65918800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr14:65918000-65918800	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr14:65918000-65918800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links