Variant report

Variant	rs11769702
Chromosome Location	chr7:65720516-65720517
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65715302..65717280-chr7:65718267..65720780,2	MCF-7	breast:
2	chr7:65719328..65723355-chr7:65725025..65727882,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10261710	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1065265	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10950026	0.95[CEU][hapmap]
rs10950029	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs10950035	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10950036	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950040	0.91[EUR][1000 genomes]
rs11766183	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11767262	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770063	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12667200	0.83[ASN][1000 genomes]
rs12668269	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12670811	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12671152	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12671834	0.80[EUR][1000 genomes]
rs12672427	0.91[EUR][1000 genomes]
rs1547529	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160641	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs17138149	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17138156	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1909508	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2173571	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279757	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2420456	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs313829	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs313830	0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs316305	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs316306	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs316323	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs316324	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs316328	0.95[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs35459055	0.91[EUR][1000 genomes]
rs3936065	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718325	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4718335	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718346	0.93[EUR][1000 genomes]
rs4718348	0.83[EUR][1000 genomes]
rs6460276	0.81[EUR][1000 genomes]
rs6460281	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6460298	0.91[EUR][1000 genomes]
rs66594357	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67775320	0.88[EUR][1000 genomes]
rs6945896	0.91[EUR][1000 genomes]
rs6960848	0.89[EUR][1000 genomes]
rs6969224	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6970498	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6979636	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73142233	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73142245	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73142265	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73146609	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73148639	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73148689	0.91[EUR][1000 genomes]
rs73150604	0.92[EUR][1000 genomes]
rs7782212	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7783889	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7785117	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7786735	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7801332	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7810213	0.92[EUR][1000 genomes]
rs7811204	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[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	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
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11769702	ZNF273	cis	cerebellum	SCAN
rs11769702	RABGEF1	cis	parietal	SCAN
rs11769702	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs11769702	GS1-124K5.4	cis	Stomach	GTEx
rs11769702	ZNF92	cis	parietal	SCAN
rs11769702	RNU6-96P	cis	Thyroid	GTEx
rs11769702	GUSB	cis	parietal	SCAN
rs11769702	GTF2IRD1P1	cis	Thyroid	GTEx
rs11769702	RABGEF1	cis	cerebellum	SCAN
rs11769702	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65701600-65729200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr7:65702400-65723600	Weak transcription	Gastric	stomach
4	chr7:65704000-65726800	Weak transcription	HSMM	muscle
5	chr7:65704200-65729200	Weak transcription	Aorta	Aorta
6	chr7:65704200-65731200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:65704400-65721800	Weak transcription	Fetal Intestine Small	intestine
8	chr7:65704400-65746800	Weak transcription	Pancreas	Pancrea
9	chr7:65705800-65729200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:65707000-65721200	Weak transcription	Fetal Kidney	kidney
11	chr7:65709800-65723400	Weak transcription	Ovary	ovary
12	chr7:65711800-65723200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:65711800-65723200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:65712800-65721800	Weak transcription	Left Ventricle	heart
15	chr7:65712800-65729200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:65714600-65720600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:65715200-65721200	Weak transcription	Liver	Liver
18	chr7:65715200-65723200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:65715600-65722400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:65716000-65721400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:65716200-65723600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:65716600-65721400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:65718000-65723200	Weak transcription	Brain Anterior Caudate	brain
24	chr7:65718600-65723200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr7:65719400-65722200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr7:65719600-65721400	Enhancers	HepG2	liver
27	chr7:65719800-65721400	Enhancers	HMEC	breast
28	chr7:65719800-65723400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:65719800-65730400	Weak transcription	Right Ventricle	heart
30	chr7:65720000-65721600	Enhancers	Osteobl	bone
31	chr7:65720200-65720600	Enhancers	Brain Angular Gyrus	brain
32	chr7:65720200-65720800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:65720200-65720800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:65720200-65720800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:65720200-65720800	Enhancers	Brain Hippocampus Middle	brain
36	chr7:65720200-65720800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr7:65720200-65720800	Enhancers	NHDF-Ad	bronchial
38	chr7:65720200-65721000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:65720200-65721000	Enhancers	HSMMtube	muscle
40	chr7:65720200-65721000	Enhancers	NHEK	skin
41	chr7:65720200-65721200	Enhancers	NH-A	brain
42	chr7:65720200-65721400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:65720200-65721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:65720200-65721400	Enhancers	NHLF	lung
45	chr7:65720200-65721800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:65720400-65720800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:65720400-65720800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:65720400-65720800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr7:65720400-65721200	Enhancers	Fetal Lung	lung
50	chr7:65720400-65721600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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