Variant report

Variant	rs73136346
Chromosome Location	chr7:65566082-65566083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65563235..65566518-chr7:65579011..65581335,3	MCF-7	breast:
2	chr7:65563649..65566683-chr7:65578224..65580127,3	MCF-7	breast:
3	chr7:65563372..65566895-chr7:65568965..65573405,4	MCF-7	breast:
4	chr7:65564438..65566579-chr7:65590943..65592744,2	MCF-7	breast:
5	chr7:65536863..65539073-chr7:65564586..65566634,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10950024	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10950025	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950027	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10950028	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10950029	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11760805	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767833	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12666485	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671834	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12673308	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160636	0.82[ASN][1000 genomes]
rs160640	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs160641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs160645	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs160647	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17138089	0.90[ASN][1000 genomes]
rs17138149	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs221986	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244226	0.83[EUR][1000 genomes]
rs2451953	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460427	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465121	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28815324	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2946580	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs313817	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs313818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313823	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313828	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs313830	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs316305	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316306	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316316	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316320	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316323	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316324	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316328	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400767	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4441996	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718325	0.86[ASN][1000 genomes]
rs6460276	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6460281	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67302640	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67397473	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67688847	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67775320	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6960870	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73142233	0.86[ASN][1000 genomes]
rs73142245	0.86[ASN][1000 genomes]
rs73376394	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73376401	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73378304	0.82[AFR][1000 genomes]
rs7782212	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7783727	0.81[ASN][1000 genomes]
rs7786728	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7786735	0.85[ASN][1000 genomes]
rs7787063	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs73136346	RNU6-96P	cis	Thyroid	GTEx
rs73136346	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs73136346	GS1-124K5.4	cis	Artery Aorta	GTEx
rs73136346	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs73136346	GTF2IRD1P1	cis	Thyroid	GTEx
rs73136346	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65558200-65569400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:65565000-65566200	Active TSS	Duodenum Mucosa	Duodenum
3	chr7:65565200-65579800	Weak transcription	Spleen	Spleen
4	chr7:65565400-65566200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:65565400-65566200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:65565600-65566200	Enhancers	Primary B cells from peripheral blood	blood
7	chr7:65565600-65566200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr7:65565600-65566200	Enhancers	Brain Substantia Nigra	brain
9	chr7:65565600-65566200	Enhancers	Pancreas	Pancrea
10	chr7:65565600-65570400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:65565600-65571200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:65565600-65571200	Weak transcription	NHDF-Ad	bronchial
13	chr7:65565600-65571400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:65565600-65571600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:65565600-65572400	Weak transcription	Lung	lung
16	chr7:65565600-65573400	Weak transcription	HepG2	liver
17	chr7:65565600-65575200	Weak transcription	Liver	Liver
18	chr7:65565600-65575800	Weak transcription	HMEC	breast
19	chr7:65565600-65575800	Weak transcription	NH-A	brain
20	chr7:65565600-65579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:65565800-65566200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:65565800-65566200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr7:65565800-65566200	Enhancers	Colonic Mucosa	Colon
24	chr7:65565800-65566200	Enhancers	Esophagus	oesophagus
25	chr7:65565800-65566200	Enhancers	Placenta	Placenta
26	chr7:65565800-65566200	Enhancers	Ovary	ovary
27	chr7:65565800-65566600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:65565800-65566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:65565800-65567200	Weak transcription	Right Atrium	heart
30	chr7:65565800-65567800	Weak transcription	NHEK	skin
31	chr7:65565800-65568200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:65565800-65570200	Weak transcription	Hela-S3	cervix
33	chr7:65565800-65571200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:65565800-65572200	Weak transcription	Fetal Intestine Small	intestine
35	chr7:65565800-65579000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:65565800-65579000	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:65565800-65579000	Weak transcription	Fetal Stomach	stomach
38	chr7:65565800-65579400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:65566000-65566200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr7:65566000-65566200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr7:65566000-65566200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr7:65566000-65566800	Enhancers	K562	blood
43	chr7:65566000-65568200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:65566000-65568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:65566000-65568800	Weak transcription	Osteobl	bone
46	chr7:65566000-65569000	Weak transcription	A549	lung
47	chr7:65566000-65579000	Weak transcription	Primary T cells from cord blood	blood

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