Variant report

Variant	rs11628094
Chromosome Location	chr14:24925789-24925790
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	chr14:24925537..24927679-chr14:24931012..24933705,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10139053	0.80[ASN][1000 genomes]
rs10146759	1.00[CHB][hapmap]
rs10220622	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs11158708	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11158709	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626219	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12433346	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884447	0.81[LWK][hapmap];0.93[MKK][hapmap]
rs12891613	1.00[CHB][hapmap]
rs1473723	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473724	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473725	0.83[AFR][1000 genomes]
rs1473726	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs17184843	0.89[CEU][hapmap]
rs1956891	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956892	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956894	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1956895	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956896	0.89[LWK][hapmap];0.99[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1956897	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012865	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012874	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038502	0.85[ASN][1000 genomes]
rs2180838	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277488	1.00[ASN][1000 genomes]
rs2277489	0.85[MKK][hapmap]
rs2332332	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332333	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs2332334	0.83[AFR][1000 genomes]
rs3759635	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4390517	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553505	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586346	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4640100	0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4981515	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981520	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982915	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982922	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982923	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4982924	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982925	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982926	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5248	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs7143047	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7149255	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7149743	0.87[LWK][hapmap];0.99[MKK][hapmap];0.80[YRI][hapmap]
rs8008309	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009695	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013354	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911369	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911370	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	nsv564061	chr14:24911138-24945331	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	n/a
5	esv2761824	chr14:24914008-24993666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
6	nsv1043355	chr14:24914008-24993666	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
7	nsv1045732	chr14:24914008-25019317	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
8	esv19772	chr14:24914740-24951857	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv523200	chr14:24915383-24975032	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv521915	chr14:24915383-24992619	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
11	nsv564062	chr14:24915383-24992619	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11628094	SDR39U1	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24912000-24925800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:24912600-24925800	Weak transcription	Ovary	ovary
3	chr14:24912800-24950800	Weak transcription	Gastric	stomach
4	chr14:24913000-24925800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr14:24913000-24926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr14:24913000-24930000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:24913000-24931600	Weak transcription	Fetal Kidney	kidney
8	chr14:24913000-24932400	Weak transcription	Primary B cells from cord blood	blood
9	chr14:24913000-24932800	Weak transcription	Primary T cells from cord blood	blood
10	chr14:24920800-24927400	Weak transcription	Spleen	Spleen
11	chr14:24922000-24925800	Weak transcription	Liver	Liver
12	chr14:24922200-24946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:24922800-24951000	Weak transcription	Pancreas	Pancrea
14	chr14:24923000-24925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr14:24923200-24937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:24923600-24932600	Weak transcription	Right Ventricle	heart
17	chr14:24924000-24929400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:24924200-24928000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:24924200-24932000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:24924600-24925800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:24924600-24927600	Weak transcription	HepG2	liver
22	chr14:24925200-24925800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:24925200-24929600	Weak transcription	Fetal Stomach	stomach
24	chr14:24925400-24926200	ZNF genes & repeats	HMEC	breast
25	chr14:24925600-24926000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:24925600-24926000	ZNF genes & repeats	Placenta	Placenta
27	chr14:24925600-24926400	ZNF genes & repeats	Aorta	Aorta
28	chr14:24925600-24926400	ZNF genes & repeats	Fetal Intestine Small	intestine

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