Variant report

Variant	rs5001609
Chromosome Location	chr6:53664396-53664397
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	chr6:53663341..53666059-chr6:53671400..53673766,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs13197492	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000998	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3001002	0.83[ASN][1000 genomes]
rs3001003	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3003489	0.83[ASN][1000 genomes]
rs3003491	0.83[ASN][1000 genomes]
rs3003493	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3003496	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3003497	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35709775	0.83[EUR][1000 genomes]
rs4236113	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4265033	0.83[ASN][1000 genomes]
rs4269375	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4276503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4342426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	0.83[ASN][1000 genomes]
rs4382260	0.83[ASN][1000 genomes]
rs4398733	0.83[ASN][1000 genomes]
rs4421195	0.81[EUR][1000 genomes]
rs4475321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484515	0.83[ASN][1000 genomes]
rs4493745	0.86[TSI][hapmap]
rs4518484	0.81[EUR][1000 genomes]
rs4587161	0.84[EUR][1000 genomes]
rs4591854	0.83[ASN][1000 genomes]
rs4712048	0.83[ASN][1000 genomes]
rs4712049	0.83[ASN][1000 genomes]
rs4715425	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715426	0.83[ASN][1000 genomes]
rs6458958	0.83[ASN][1000 genomes]
rs6458959	0.83[ASN][1000 genomes]
rs6458960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458961	0.83[ASN][1000 genomes]
rs6458962	0.83[ASN][1000 genomes]
rs6458966	0.83[ASN][1000 genomes]
rs6458970	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6650996	0.83[ASN][1000 genomes]
rs6900929	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6920743	0.83[ASN][1000 genomes]
rs6934444	0.83[EUR][1000 genomes]
rs7762883	0.83[ASN][1000 genomes]
rs7763147	0.83[ASN][1000 genomes]
rs7767443	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349686	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357774	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357775	0.80[EUR][1000 genomes]
rs9367542	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9370236	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382239	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5001609	LRRC1	cis	parietal	SCAN
rs5001609	COL21A1	cis	cerebellum	SCAN
rs5001609	PKHD1	cis	parietal	SCAN
rs5001609	C6orf142	cis	cerebellum	SCAN
rs5001609	PRIM2	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
3	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53661400-53668000	Weak transcription	Ovary	ovary
6	chr6:53661400-53669800	Weak transcription	Gastric	stomach
7	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
10	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:53661600-53665800	Weak transcription	NHLF	lung
12	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:53662200-53665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:53662400-53664600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:53662400-53668000	Weak transcription	NH-A	brain
18	chr6:53662600-53664800	Enhancers	HepG2	liver
19	chr6:53662600-53665800	Weak transcription	Brain Anterior Caudate	brain
20	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
23	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
25	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
26	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
27	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:53662800-53668000	Weak transcription	NHEK	skin
30	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:53662800-53669800	Weak transcription	HMEC	breast
32	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
33	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:53663000-53664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
38	chr6:53663400-53664800	Enhancers	Fetal Thymus	thymus
39	chr6:53663600-53664800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53663600-53664800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:53663600-53664800	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:53664000-53664400	Active TSS	Colonic Mucosa	Colon
43	chr6:53664000-53664600	Enhancers	Colon Smooth Muscle	Colon
44	chr6:53664000-53664800	Enhancers	Brain Hippocampus Middle	brain
45	chr6:53664000-53664800	Genic enhancers	Dnd41	blood
46	chr6:53664000-53665000	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:53664000-53668000	Weak transcription	HUVEC	blood vessel
48	chr6:53664000-53669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:53664200-53664400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:53664200-53664400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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