Variant report

Variant	rs7767443
Chromosome Location	chr6:53744589-53744590
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53658255..53661038-chr6:53744505..53747227,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs13197492	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3000998	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3001002	0.81[ASN][1000 genomes]
rs3001003	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3003489	0.81[ASN][1000 genomes]
rs3003491	0.81[ASN][1000 genomes]
rs3003493	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3003497	0.90[ASN][1000 genomes]
rs4236113	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4265033	0.81[ASN][1000 genomes]
rs4269375	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4276503	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4342426	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4351263	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs4382260	0.81[ASN][1000 genomes]
rs4398733	0.81[ASN][1000 genomes]
rs4475321	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4484515	0.81[ASN][1000 genomes]
rs4493745	0.82[TSI][hapmap]
rs4587161	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4591854	0.81[ASN][1000 genomes]
rs4712048	0.81[ASN][1000 genomes]
rs4712049	0.81[ASN][1000 genomes]
rs4715425	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]
rs4715426	0.81[ASN][1000 genomes]
rs4715431	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5001609	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6458958	0.81[ASN][1000 genomes]
rs6458959	0.81[ASN][1000 genomes]
rs6458960	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6458961	0.81[ASN][1000 genomes]
rs6458962	0.81[ASN][1000 genomes]
rs6458966	0.81[ASN][1000 genomes]
rs6458970	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6650996	0.81[ASN][1000 genomes]
rs6900929	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6920743	0.81[ASN][1000 genomes]
rs7762883	0.81[ASN][1000 genomes]
rs7763147	0.81[ASN][1000 genomes]
rs9349686	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357774	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357775	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9367542	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9370236	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9382239	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]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7767443	PKHD1	cis	parietal	SCAN
rs7767443	LRRC1	cis	parietal	SCAN
rs7767443	PRIM2	cis	parietal	SCAN
rs7767443	C6orf142	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
5	chr6:53729400-53748000	Weak transcription	HepG2	liver
6	chr6:53730200-53748200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
8	chr6:53732000-53747800	Weak transcription	HSMMtube	muscle
9	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
10	chr6:53735000-53751800	Weak transcription	Gastric	stomach
11	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
12	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:53737800-53744800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
15	chr6:53738400-53747800	Weak transcription	Fetal Thymus	thymus
16	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:53739000-53753600	Weak transcription	NHEK	skin
18	chr6:53739000-53767800	Weak transcription	Ovary	ovary
19	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
20	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:53740200-53747800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:53740400-53754000	Weak transcription	HSMM	muscle
25	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:53742000-53744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:53742200-53745200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:53742200-53748000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
31	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
32	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:53742600-53748000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:53743400-53744800	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:53743600-53744600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:53743600-53744600	Weak transcription	Lung	lung
38	chr6:53744000-53744800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
40	chr6:53744200-53744600	Strong transcription	Fetal Intestine Small	intestine
41	chr6:53744200-53744800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:53744200-53752200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:53744400-53748200	Weak transcription	Dnd41	blood

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