Variant report

Variant	rs4613824
Chromosome Location	chr6:53742923-53742924
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	chr6:53731424..53733383-chr6:53740788..53743040,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10948779	0.84[CEU][hapmap]
rs13220665	1.00[YRI][hapmap]
rs2745462	0.81[CEU][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2820215	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2820216	0.84[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3000997	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs3000999	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs3001009	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs3003493	0.84[CEU][hapmap]
rs3813849	1.00[YRI][hapmap]
rs4236113	0.84[CEU][hapmap]
rs4236115	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4351263	0.84[CEU][hapmap]
rs4489155	1.00[YRI][hapmap]
rs6458971	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458972	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6901644	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs742524	0.84[CEU][hapmap]
rs7774173	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9296721	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9367544	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9370239	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9382234	1.00[YRI][hapmap]
rs9382250	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9395886	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
6	chr6:53729400-53748000	Weak transcription	HepG2	liver
7	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:53730400-53743800	Weak transcription	Fetal Heart	heart
10	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
11	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
12	chr6:53735000-53751800	Weak transcription	Gastric	stomach
13	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
14	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
15	chr6:53737800-53744800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
17	chr6:53738400-53747800	Weak transcription	Fetal Thymus	thymus
18	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53739000-53753600	Weak transcription	NHEK	skin
20	chr6:53739000-53767800	Weak transcription	Ovary	ovary
21	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
22	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:53740200-53747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:53740400-53754000	Weak transcription	HSMM	muscle
27	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:53741000-53743800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:53741800-53743800	Weak transcription	Dnd41	blood
30	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:53742000-53744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:53742200-53745200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:53742200-53748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
35	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
36	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:53742600-53748000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:53742800-53744200	Weak transcription	Fetal Intestine Small	intestine

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