Variant report

Variant	rs9463988
Chromosome Location	chr6:53720713-53720714
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	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:
2	chr6:53720118..53721729-chr6:53744956..53746701,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11759220	0.92[ASN][1000 genomes]
rs12661475	0.89[ASN][1000 genomes]
rs12663216	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2050159	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3001004	0.88[ASN][1000 genomes]
rs3001005	0.89[ASN][1000 genomes]
rs3001006	0.89[ASN][1000 genomes]
rs3001007	0.88[ASN][1000 genomes]
rs3001008	0.88[ASN][1000 genomes]
rs3003488	0.88[ASN][1000 genomes]
rs3003490	0.88[ASN][1000 genomes]
rs3003492	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs3003494	0.88[ASN][1000 genomes]
rs3003498	0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs35081045	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4254992	0.88[ASN][1000 genomes]
rs4273680	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs4478409	0.86[JPT][hapmap]
rs4486000	0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4540263	0.90[ASN][1000 genomes]
rs4582388	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4618525	0.88[ASN][1000 genomes]
rs4624872	0.81[CHB][hapmap]
rs4640878	0.89[ASN][1000 genomes]
rs4715427	0.83[ASN][1000 genomes]
rs4715428	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715429	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60467893	0.88[ASN][1000 genomes]
rs62397076	0.87[ASN][1000 genomes]
rs6905323	0.81[ASN][1000 genomes]
rs6905563	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs6906326	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6906921	0.81[CHB][hapmap]
rs6907027	0.81[CHB][hapmap]
rs6909040	0.90[ASN][1000 genomes]
rs6909094	0.90[ASN][1000 genomes]
rs6916929	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6925391	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761285	0.80[ASN][1000 genomes]
rs9296720	0.92[ASN][1000 genomes]
rs9349684	0.82[ASN][1000 genomes]
rs9367543	0.80[ASN][1000 genomes]
rs9382245	0.80[ASN][1000 genomes]
rs9395890	0.81[CEU][hapmap]
rs9395891	0.81[CEU][hapmap]
rs9463996	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9474643	0.83[JPT][hapmap]
rs9474661	0.88[ASN][1000 genomes]
rs9474665	0.90[ASN][1000 genomes]
rs9474671	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9474680	0.84[AMR][1000 genomes];0.88[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9463988	LRRC1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
4	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
8	chr6:53712800-53721600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:53713000-53722000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:53718400-53721200	Enhancers	Fetal Intestine Small	intestine
12	chr6:53718400-53723400	Enhancers	Stomach Mucosa	stomach
13	chr6:53718600-53721400	Enhancers	Duodenum Mucosa	Duodenum
14	chr6:53718800-53721200	Enhancers	Fetal Intestine Large	intestine
15	chr6:53718800-53723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:53719000-53720800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr6:53719200-53720800	Enhancers	HMEC	breast
18	chr6:53719800-53720800	Enhancers	Small Intestine	intestine
19	chr6:53719800-53721600	Enhancers	Fetal Heart	heart
20	chr6:53719800-53722000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
22	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
23	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
24	chr6:53720000-53721000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:53720000-53721400	Enhancers	HSMMtube	muscle
26	chr6:53720000-53721800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr6:53720000-53722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:53720000-53723000	Enhancers	Left Ventricle	heart
29	chr6:53720000-53724000	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:53720000-53724400	Enhancers	Brain Anterior Caudate	brain
31	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:53720200-53720800	Enhancers	Fetal Muscle Leg	muscle
33	chr6:53720200-53721800	Enhancers	Aorta	Aorta
34	chr6:53720200-53721800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:53720200-53722200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:53720200-53722400	Enhancers	Brain Angular Gyrus	brain
37	chr6:53720200-53722600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:53720200-53723000	Enhancers	Right Atrium	heart
39	chr6:53720200-53723000	Enhancers	Right Ventricle	heart
40	chr6:53720400-53720800	Genic enhancers	Fetal Thymus	thymus
41	chr6:53720400-53721000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:53720400-53721000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr6:53720400-53721200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:53720400-53721600	Weak transcription	HUVEC	blood vessel
45	chr6:53720400-53722800	Enhancers	HepG2	liver
46	chr6:53720400-53723000	Enhancers	Gastric	stomach
47	chr6:53720600-53721400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:53720600-53721600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:53720600-53721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:53720600-53721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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