Variant report

Variant	rs854317
Chromosome Location	chr14:25319589-25319590
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1241650	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12586290	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs17185151	0.87[ASN][1000 genomes]
rs17257382	0.94[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1957759	0.82[YRI][hapmap]
rs1958352	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1974008	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs2297060	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs35990769	0.87[ASN][1000 genomes]
rs3759644	0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs712491	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs712492	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs854312	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs854313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854318	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854320	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs854323	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854324	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854326	0.84[LWK][hapmap]
rs854327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs861258	0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv901506	chr14:25295551-25377188	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25288600-25322800	Weak transcription	Placenta	Placenta
2	chr14:25306600-25321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:25309000-25328000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr14:25309800-25323000	Weak transcription	Pancreas	Pancrea
5	chr14:25309800-25324400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:25310000-25321000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:25310200-25320800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr14:25313800-25320800	Weak transcription	Left Ventricle	heart
9	chr14:25313800-25323400	Weak transcription	Small Intestine	intestine
10	chr14:25314600-25333600	Weak transcription	Lung	lung
11	chr14:25315000-25319600	Enhancers	Brain Anterior Caudate	brain
12	chr14:25315400-25320800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:25315600-25320800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr14:25315600-25321000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:25315600-25321400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr14:25315600-25330400	Weak transcription	Brain Angular Gyrus	brain
17	chr14:25315800-25320200	Weak transcription	Fetal Intestine Large	intestine
18	chr14:25315800-25320800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr14:25315800-25320800	Weak transcription	HepG2	liver
20	chr14:25315800-25324200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:25316000-25320800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:25316000-25330400	Weak transcription	Brain Hippocampus Middle	brain
23	chr14:25316600-25320800	Weak transcription	Fetal Intestine Small	intestine
24	chr14:25316800-25320200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:25317000-25320000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:25317400-25319600	Enhancers	NHDF-Ad	bronchial
27	chr14:25317800-25323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr14:25317800-25344000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:25318000-25321200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:25318000-25328400	Weak transcription	Right Ventricle	heart
31	chr14:25318200-25319600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr14:25318200-25320000	Enhancers	HSMMtube	muscle
33	chr14:25318200-25330200	Weak transcription	Fetal Heart	heart
34	chr14:25318400-25321200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr14:25318400-25321400	Weak transcription	Osteobl	bone
36	chr14:25319000-25320000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr14:25319000-25320800	Weak transcription	NH-A	brain
38	chr14:25319000-25330400	Weak transcription	Adipose Nuclei	Adipose
39	chr14:25319200-25319600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr14:25319200-25319600	Weak transcription	Fetal Lung	lung
41	chr14:25319200-25320000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr14:25319200-25320800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr14:25319200-25321400	Weak transcription	HSMM	muscle
44	chr14:25319400-25319600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr14:25319400-25319800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:25319400-25321600	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links