Variant report

Variant	rs6905323
Chromosome Location	chr6:53729761-53729762
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	chr6:53717928..53719756-chr6:53728412..53730149,2	MCF-7	breast:
2	chr6:53664494..53666032-chr6:53727700..53729812,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10948787	0.82[EUR][1000 genomes]
rs11759220	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11759427	0.83[GIH][hapmap];0.87[MEX][hapmap]
rs12661475	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12661938	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12663216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1883632	0.89[CHB][hapmap]
rs2050159	0.83[ASN][1000 genomes]
rs2076496	0.81[EUR][1000 genomes]
rs3001004	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3001005	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3001006	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3001007	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3001008	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003488	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003490	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003494	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3003498	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3813850	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs4254992	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4273680	0.85[CHD][hapmap];0.80[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4540263	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4618525	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4640878	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4712050	0.81[EUR][1000 genomes]
rs4715427	0.94[EUR][1000 genomes]
rs4715429	0.81[ASN][1000 genomes]
rs60467893	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62397076	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62397090	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6905563	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6906326	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs6909040	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6909094	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6916929	0.86[ASN][1000 genomes]
rs6925391	0.81[ASN][1000 genomes]
rs7750173	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296720	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463983	0.95[EUR][1000 genomes]
rs9463988	0.81[ASN][1000 genomes]
rs9463996	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9463997	0.84[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9474643	0.82[CHB][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs9474661	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9474665	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9474671	0.85[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6905323	LRRC1	cis	multi-tissue	Pritchard
rs6905323	BCL7A	trans	lymphoblastoid	seeQTL

Chromatin state (count:46 , 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	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:53720600-53741400	Weak transcription	Dnd41	blood
6	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
7	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:53723400-53736800	Weak transcription	Stomach Mucosa	stomach
9	chr6:53725400-53730000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr6:53725400-53730200	Enhancers	Brain Anterior Caudate	brain
11	chr6:53725400-53730400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:53725800-53730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:53726400-53730200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:53726600-53730200	Enhancers	Rectal Smooth Muscle	rectum
15	chr6:53726600-53730400	Enhancers	Fetal Brain Male	brain
16	chr6:53726800-53729800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:53727400-53729800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr6:53727600-53730000	Enhancers	Brain Angular Gyrus	brain
19	chr6:53727600-53730400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr6:53727600-53731200	Weak transcription	Aorta	Aorta
21	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
22	chr6:53728000-53730000	Enhancers	Right Atrium	heart
23	chr6:53728000-53731400	Enhancers	Brain Substantia Nigra	brain
24	chr6:53728200-53732000	Enhancers	Brain Hippocampus Middle	brain
25	chr6:53728200-53734200	Weak transcription	HUVEC	blood vessel
26	chr6:53728400-53730000	Enhancers	HSMMtube	muscle
27	chr6:53728400-53731000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:53728400-53731400	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:53728400-53734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:53728600-53730000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:53728600-53730800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:53728600-53738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:53728600-53738600	Weak transcription	NHEK	skin
34	chr6:53728800-53729800	Enhancers	Left Ventricle	heart
35	chr6:53728800-53730400	Enhancers	Fetal Heart	heart
36	chr6:53729000-53732200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:53729000-53733600	Weak transcription	Fetal Stomach	stomach
38	chr6:53729000-53734800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53729000-53734800	Weak transcription	HMEC	breast
40	chr6:53729400-53730000	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:53729400-53730200	Weak transcription	Brain Germinal Matrix	brain
42	chr6:53729400-53731200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:53729400-53736600	Weak transcription	Fetal Intestine Small	intestine
44	chr6:53729400-53738800	Weak transcription	Pancreas	Pancrea
45	chr6:53729400-53748000	Weak transcription	HepG2	liver
46	chr6:53729600-53734400	Weak transcription	Colon Smooth Muscle	Colon

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