Variant report

Variant	rs4715425
Chromosome Location	chr6:53676354-53676355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53657579..53660733-chr6:53674241..53678049,6	MCF-7	breast:
2	chr6:53329814..53330329-chr6:53676241..53676983,3	MCF-7	breast:
3	chr6:53329635..53330329-chr6:53676241..53677108,3	MCF-7	breast:
4	chr6:53588027..53590620-chr6:53675669..53678421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13197492	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000998	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3001002	0.85[ASN][1000 genomes]
rs3001003	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003489	0.85[ASN][1000 genomes]
rs3003491	0.85[ASN][1000 genomes]
rs3003493	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs3003496	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3003497	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35709775	0.83[EUR][1000 genomes]
rs4236113	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4265033	0.85[ASN][1000 genomes]
rs4269375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4276503	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4342426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4351263	0.85[ASN][1000 genomes]
rs4382260	0.85[ASN][1000 genomes]
rs4398733	0.85[ASN][1000 genomes]
rs4421195	0.81[EUR][1000 genomes]
rs4475321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484515	0.85[ASN][1000 genomes]
rs4493745	0.86[TSI][hapmap]
rs4518484	0.81[EUR][1000 genomes]
rs4587161	0.85[EUR][1000 genomes]
rs4591854	0.85[ASN][1000 genomes]
rs4712048	0.85[ASN][1000 genomes]
rs4712049	0.85[ASN][1000 genomes]
rs4715426	0.85[ASN][1000 genomes]
rs5001609	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458958	0.85[ASN][1000 genomes]
rs6458959	0.85[ASN][1000 genomes]
rs6458960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458961	0.85[ASN][1000 genomes]
rs6458962	0.85[ASN][1000 genomes]
rs6458966	0.85[ASN][1000 genomes]
rs6458970	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6650996	0.85[ASN][1000 genomes]
rs6900929	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6920743	0.85[ASN][1000 genomes]
rs6934444	0.84[EUR][1000 genomes]
rs7762883	0.85[ASN][1000 genomes]
rs7763147	0.85[ASN][1000 genomes]
rs7767443	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349686	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357774	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357775	0.81[EUR][1000 genomes]
rs9367542	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370236	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4715425	LRRC1	cis	parietal	SCAN
rs4715425	C6orf142	cis	cerebellum	SCAN
rs4715425	PRIM2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
3	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
5	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:53668800-53683800	Weak transcription	Ovary	ovary
7	chr6:53669800-53676800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:53670200-53678000	Weak transcription	Aorta	Aorta
9	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:53671000-53676400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
16	chr6:53671400-53676400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:53673000-53678400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:53673600-53677800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:53673600-53682800	Weak transcription	Dnd41	blood
22	chr6:53673800-53678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:53674200-53678200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:53674600-53677200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:53674800-53678400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:53674800-53679600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
28	chr6:53675000-53676400	Enhancers	Brain Germinal Matrix	brain
29	chr6:53675000-53676600	Enhancers	HepG2	liver
30	chr6:53675000-53677000	Enhancers	HMEC	breast
31	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
32	chr6:53675400-53677000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:53675400-53679000	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
35	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:53675600-53676400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:53675600-53676400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:53675600-53676400	Enhancers	Brain Angular Gyrus	brain
39	chr6:53675600-53676400	Enhancers	Colonic Mucosa	Colon
40	chr6:53675600-53676400	Enhancers	A549	lung
41	chr6:53675600-53676400	Enhancers	GM12878-XiMat	blood
42	chr6:53675600-53676400	Flanking Active TSS	NHEK	skin
43	chr6:53675600-53676800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:53675600-53676800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:53675600-53676800	Enhancers	Pancreas	Pancrea
46	chr6:53675600-53677000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr6:53675600-53677000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:53675600-53677000	Enhancers	Fetal Intestine Large	intestine
49	chr6:53675600-53678200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr6:53675600-53678800	Enhancers	Hela-S3	cervix

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