Variant report

Variant	rs11748504
Chromosome Location	chr5:52247276-52247277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52246465..52248425-chr5:52385773..52388530,2	MCF-7	breast:
2	chr5:52244780..52247572-chr5:52249796..52252128,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738606	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739571	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742694	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742813	0.89[EUR][1000 genomes]
rs11745309	0.91[YRI][hapmap]
rs11749081	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12186544	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13156420	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13165509	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13179969	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180488	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421943	0.88[EUR][1000 genomes]
rs3212383	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3212656	0.84[EUR][1000 genomes]
rs34288275	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34352729	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34512129	0.88[EUR][1000 genomes]
rs34865297	0.87[EUR][1000 genomes]
rs35597318	0.88[EUR][1000 genomes]
rs35657730	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35862618	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35926366	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865755	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs6859171	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702766	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7713782	0.84[EUR][1000 genomes]
rs9791046	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv830295	chr5:52084532-52257696	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv1794366	chr5:52240421-52249476	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3434707	chr5:52247217-52247453	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52202200-52252200	Weak transcription	Small Intestine	intestine
2	chr5:52220600-52252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:52221400-52251800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52232800-52249800	Weak transcription	Left Ventricle	heart
5	chr5:52238800-52252200	Strong transcription	Liver	Liver
6	chr5:52240000-52249800	Weak transcription	Aorta	Aorta
7	chr5:52240000-52253000	Weak transcription	Right Ventricle	heart
8	chr5:52240000-52253400	Weak transcription	Esophagus	oesophagus
9	chr5:52240000-52253600	Weak transcription	Lung	lung
10	chr5:52240200-52251800	Weak transcription	Fetal Intestine Small	intestine
11	chr5:52240200-52253400	Weak transcription	Spleen	Spleen
12	chr5:52240400-52251800	Weak transcription	Fetal Intestine Large	intestine
13	chr5:52241200-52252000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:52241400-52247600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:52242400-52247600	Enhancers	NHEK	skin
16	chr5:52242600-52247600	Enhancers	HMEC	breast
17	chr5:52243400-52248200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:52243400-52252600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:52244200-52247600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:52244400-52247400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:52244800-52250800	Weak transcription	HepG2	liver
22	chr5:52244800-52253600	Weak transcription	Fetal Stomach	stomach
23	chr5:52245000-52251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:52245200-52249800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:52245200-52253400	Weak transcription	HSMMtube	muscle
26	chr5:52245400-52251000	Weak transcription	NHDF-Ad	bronchial
27	chr5:52245600-52247800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:52245600-52252600	Weak transcription	Dnd41	blood
29	chr5:52245800-52251600	Weak transcription	Placenta	Placenta
30	chr5:52245800-52253000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:52246000-52254400	Weak transcription	Fetal Kidney	kidney
32	chr5:52246200-52251800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:52246200-52254200	Weak transcription	Fetal Lung	lung
34	chr5:52246400-52249800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:52246600-52249000	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:52246800-52249000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:52246800-52253600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:52247000-52248600	Weak transcription	Adipose Nuclei	Adipose
39	chr5:52247000-52253000	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links