Variant report

Variant	rs3759642
Chromosome Location	chr14:25289410-25289411
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	chr12:79510182..79510824-chr14:25288938..25289510,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10133078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10136693	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10138734	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12433081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1381318	0.85[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1381319	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17109336	1.00[MEX][hapmap]
rs1887935	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297059	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2877685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55951119	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6574033	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs749595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs766668	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007336	0.94[ASW][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs8014742	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8016612	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs872978	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs872979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs9319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25285200-25302200	Weak transcription	HSMM	muscle
2	chr14:25285800-25297800	Weak transcription	HSMMtube	muscle
3	chr14:25286000-25296800	Weak transcription	Esophagus	oesophagus
4	chr14:25287400-25306200	Weak transcription	Brain Anterior Caudate	brain
5	chr14:25287600-25290200	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr14:25287800-25292200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr14:25287800-25306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:25288000-25291600	Enhancers	Fetal Intestine Large	intestine
9	chr14:25288000-25309400	Weak transcription	Lung	lung
10	chr14:25288400-25289800	Weak transcription	Right Atrium	heart
11	chr14:25288400-25290000	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr14:25288400-25290000	Genic enhancers	HepG2	liver
13	chr14:25288400-25304400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr14:25288400-25309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:25288600-25289600	Weak transcription	Fetal Heart	heart
16	chr14:25288600-25290200	Enhancers	Liver	Liver
17	chr14:25288600-25291000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr14:25288600-25291600	Enhancers	Fetal Intestine Small	intestine
19	chr14:25288600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr14:25288600-25302200	Weak transcription	Left Ventricle	heart
21	chr14:25288600-25322800	Weak transcription	Placenta	Placenta
22	chr14:25288800-25308000	Weak transcription	Fetal Lung	lung
23	chr14:25288800-25317400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr14:25289200-25289600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr14:25289200-25290000	Weak transcription	Right Ventricle	heart
26	chr14:25289200-25309400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links