Variant report

Variant	rs12516733
Chromosome Location	chr5:52941835-52941836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12513928	1.00[CEU][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]
rs12514182	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515547	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12518536	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519736	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522533	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523552	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388111	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs17305186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994648	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045391	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054970	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087619	0.94[YRI][hapmap]
rs2406914	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56743978	0.82[AFR][1000 genomes]
rs58919751	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72750157	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72750158	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751823	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72751826	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72751865	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72751870	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753665	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72753667	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753681	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72753683	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72753687	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72753690	0.83[AMR][1000 genomes];0.92[EUR][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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881348	chr5:52885100-52942083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881237	chr5:52885100-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv880426	chr5:52885100-52953048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv880762	chr5:52894276-52944428	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52903000-52943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:52904400-52966600	Weak transcription	Osteobl	bone
3	chr5:52919200-52944000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:52921600-52963400	Weak transcription	A549	lung
6	chr5:52922000-52942000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:52925600-52961200	Weak transcription	Esophagus	oesophagus
8	chr5:52925800-52952000	Weak transcription	Colonic Mucosa	Colon
9	chr5:52926000-52943800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:52926600-52948800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:52926800-52963600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:52927400-52945000	Weak transcription	Fetal Brain Female	brain
13	chr5:52927400-52961000	Weak transcription	Placenta	Placenta
14	chr5:52927600-52942400	Weak transcription	Fetal Thymus	thymus
15	chr5:52927800-52948600	Weak transcription	Pancreas	Pancrea
16	chr5:52927800-52961200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:52927800-52961200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:52927800-52961200	Weak transcription	Thymus	Thymus
19	chr5:52928000-52945000	Weak transcription	Fetal Intestine Small	intestine
20	chr5:52928000-52946000	Weak transcription	Gastric	stomach
21	chr5:52928000-52962200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:52928200-52944000	Weak transcription	GM12878-XiMat	blood
23	chr5:52928400-52942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:52928600-52944400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:52929200-52942000	Weak transcription	Dnd41	blood
27	chr5:52929200-52943200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:52929200-52947600	Weak transcription	Right Ventricle	heart
29	chr5:52929400-52944400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:52929400-52964600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:52931000-52944600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:52933200-52943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:52933200-52951600	Weak transcription	Aorta	Aorta
34	chr5:52935200-52978000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:52936600-52942000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:52936600-52943200	Weak transcription	Fetal Intestine Large	intestine
37	chr5:52936600-52944000	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:52936600-52948400	Weak transcription	Lung	lung
39	chr5:52936800-52942000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:52936800-52942000	Weak transcription	Liver	Liver
41	chr5:52936800-52943000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:52936800-52943000	Weak transcription	Left Ventricle	heart
43	chr5:52936800-52943200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:52936800-52943400	Weak transcription	Primary T cells from cord blood	blood
45	chr5:52937200-52942200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr5:52937200-52942200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr5:52937200-52944000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:52937200-52944400	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:52937200-52963600	Weak transcription	NHLF	lung
50	chr5:52937400-52942000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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