Variant report

Variant	rs55931905
Chromosome Location	chr6:53661908-53661909
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:53661660-53661939	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:53661615-53661944	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr6:53661875-53662255	HepG2	liver:	n/a	chr6:53662044-53662059
4	FOS	chr6:53661525-53662060	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr6:53661532-53662018	Hela-S3	cervix:	n/a	chr6:53661952-53661963 chr6:53661690-53661701
6	STAT3	chr6:53661601-53662106	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814
7	STAT3	chr6:53661626-53662097	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814
8	MYC	chr6:53661803-53662048	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:53661432-53662079	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr6:53661618-53662125	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814

No.	Distal block	Cell Line	Cell type
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:
2	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:
3	chr6:53652474..53654178-chr6:53661361..53663423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	TF binding region
ENSG00000137269	Chromatin interaction
ENSG00000227885	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10456165	0.87[ASN][1000 genomes]
rs10456673	0.87[ASN][1000 genomes]
rs10456674	0.87[ASN][1000 genomes]
rs10948782	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10948785	0.87[AMR][1000 genomes]
rs11968082	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11970064	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12192118	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12192689	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12195491	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12200971	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12201245	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12201913	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12202128	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12202762	0.87[ASN][1000 genomes]
rs12204130	0.87[ASN][1000 genomes]
rs12206209	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12211130	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12211417	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12211478	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12213577	0.87[ASN][1000 genomes]
rs12214863	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12216441	0.87[ASN][1000 genomes]
rs13205690	0.87[ASN][1000 genomes]
rs13211528	0.87[ASN][1000 genomes]
rs17748374	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34113003	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34876933	0.84[ASN][1000 genomes]
rs35078422	0.87[ASN][1000 genomes]
rs35143842	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35971619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935663	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4373362	0.87[ASN][1000 genomes]
rs4389767	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4639324	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55678884	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919015	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72941941	0.87[ASN][1000 genomes]
rs7739668	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7745930	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7762326	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55931905	LRRC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:53658000-53662000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr6:53659000-53662000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:53660400-53662000	Flanking Active TSS	HUVEC	blood vessel
5	chr6:53660400-53663000	Flanking Active TSS	Dnd41	blood
6	chr6:53660800-53662800	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:53660800-53663000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:53661000-53662200	Flanking Active TSS	HMEC	breast
9	chr6:53661200-53662000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:53661200-53662200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:53661200-53662400	Flanking Active TSS	NHEK	skin
12	chr6:53661200-53662600	Active TSS	Fetal Brain Female	brain
13	chr6:53661400-53662000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:53661400-53662200	Weak transcription	Esophagus	oesophagus
15	chr6:53661400-53662200	Weak transcription	Pancreas	Pancrea
16	chr6:53661400-53662600	Flanking Active TSS	HepG2	liver
17	chr6:53661400-53662800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:53661400-53663600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
20	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
21	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:53661400-53668000	Weak transcription	Ovary	ovary
24	chr6:53661400-53669800	Weak transcription	Gastric	stomach
25	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
26	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
28	chr6:53661600-53662000	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr6:53661600-53662000	Weak transcription	Small Intestine	intestine
30	chr6:53661600-53662000	Weak transcription	Thymus	Thymus
31	chr6:53661600-53662200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:53661600-53662200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:53661600-53662200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:53661600-53662200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr6:53661600-53662200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:53661600-53662400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:53661600-53662400	Enhancers	NH-A	brain
38	chr6:53661600-53662600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53661600-53662600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:53661600-53662600	Enhancers	Brain Angular Gyrus	brain
41	chr6:53661600-53662600	Enhancers	Brain Anterior Caudate	brain
42	chr6:53661600-53662600	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr6:53661600-53662600	Enhancers	Stomach Mucosa	stomach
44	chr6:53661600-53662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:53661600-53662800	Enhancers	Fetal Kidney	kidney
46	chr6:53661600-53663600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:53661600-53663600	Weak transcription	Colonic Mucosa	Colon
48	chr6:53661600-53664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:53661600-53665800	Weak transcription	NHLF	lung

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