Variant report

Variant	rs4549481
Chromosome Location	chr5:52927822-52927823
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52908310..52911077-chr5:52926707..52930021,3	MCF-7	breast:
2	chr5:52861548..52863990-chr5:52926971..52929955,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513019	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738542	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11740228	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11740800	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743262	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749849	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881514	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881524	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16881561	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847471	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2087618	0.88[AFR][1000 genomes]
rs28855127	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3958630	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4147735	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147739	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147742	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147744	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4640749	0.89[ASN][1000 genomes]
rs55828101	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6892641	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72750138	0.82[ASN][1000 genomes]
rs72750151	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751832	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751833	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751838	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72751849	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72753647	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753680	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72755395	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757304	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757372	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757390	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7716949	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729894	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv4828	chr5:52895470-52940279	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	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
12	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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52899400-52928400	Weak transcription	Fetal Heart	heart
2	chr5:52900800-52936600	Weak transcription	NHEK	skin
3	chr5:52901000-52932600	Weak transcription	Aorta	Aorta
4	chr5:52903000-52943800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr5:52903200-52939200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:52904200-52936800	Weak transcription	NHDF-Ad	bronchial
7	chr5:52904400-52966600	Weak transcription	Osteobl	bone
8	chr5:52904600-52937000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:52905000-52928800	Weak transcription	HSMM	muscle
10	chr5:52909600-52937600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:52910600-52941000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:52919200-52944000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:52920000-52936000	Weak transcription	Liver	Liver
14	chr5:52920800-52940800	Weak transcription	HepG2	liver
15	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:52921000-52936200	Weak transcription	Psoas Muscle	Psoas
17	chr5:52921000-52941800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:52921200-52937000	Weak transcription	Brain Substantia Nigra	brain
19	chr5:52921400-52936400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:52921600-52963400	Weak transcription	A549	lung
21	chr5:52922000-52936600	Weak transcription	Fetal Lung	lung
22	chr5:52922000-52939400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:52922000-52942000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:52924600-52928400	Weak transcription	Right Ventricle	heart
25	chr5:52925400-52935800	Weak transcription	Fetal Intestine Large	intestine
26	chr5:52925600-52932600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:52925600-52961200	Weak transcription	Esophagus	oesophagus
28	chr5:52925800-52928800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:52925800-52936200	Weak transcription	HSMMtube	muscle
30	chr5:52925800-52952000	Weak transcription	Colonic Mucosa	Colon
31	chr5:52926000-52941800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:52926000-52943800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:52926400-52929800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:52926400-52936400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:52926600-52928000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:52926600-52929400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:52926600-52948800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:52926800-52928000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:52926800-52928000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr5:52926800-52928000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:52926800-52928400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:52926800-52928400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:52926800-52928600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr5:52926800-52963600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr5:52927000-52928000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:52927000-52928000	Strong transcription	Adipose Nuclei	Adipose
47	chr5:52927000-52928000	Genic enhancers	Gastric	stomach
48	chr5:52927000-52928000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:52927000-52928200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:52927000-52928400	Strong transcription	Fetal Muscle Trunk	muscle

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