Variant report

Variant	rs7783889
Chromosome Location	chr7:65748353-65748354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10261710	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1065265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950026	1.00[CEU][hapmap]
rs10950027	0.81[EUR][1000 genomes]
rs10950029	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10950035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950036	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950040	0.89[EUR][1000 genomes]
rs11763224	0.85[EUR][1000 genomes]
rs11766183	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11767262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769702	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]
rs11770063	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12667200	0.90[ASN][1000 genomes]
rs12668269	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670811	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671152	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12671834	0.82[EUR][1000 genomes]
rs12672427	0.89[EUR][1000 genomes]
rs1547529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs160641	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs17138149	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17138156	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1909508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088655	0.82[YRI][hapmap]
rs2173571	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279757	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313818	0.94[YRI][hapmap]
rs313829	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs313830	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs316305	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs316306	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs316323	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs316324	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs316328	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs35459055	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3735147	0.89[EUR][1000 genomes]
rs3936065	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718325	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4718335	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718346	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4718348	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6460276	0.82[EUR][1000 genomes]
rs6460281	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6460298	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66594357	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67775320	0.89[EUR][1000 genomes]
rs6945896	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6947339	0.82[YRI][hapmap]
rs6950988	0.85[EUR][1000 genomes]
rs6960848	0.89[EUR][1000 genomes]
rs6969224	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6970498	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73142233	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73142245	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73142265	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73146609	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73148639	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73148689	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73150604	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73376394	0.80[EUR][1000 genomes]
rs73376401	0.81[EUR][1000 genomes]
rs7782212	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7785117	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7786735	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778697	0.82[YRI][hapmap]
rs778720	0.85[YRI][hapmap]
rs778736	0.82[YRI][hapmap]
rs7801332	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7810213	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7811204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7783889	GS1-124K5.4	cis	Artery Aorta	GTEx
rs7783889	RNU6-96P	cis	Thyroid	GTEx
rs7783889	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs7783889	GS1-124K5.11	cis	Thyroid	GTEx
rs7783889	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs7783889	GTF2IRD1P1	cis	Thyroid	GTEx
rs7783889	GS1-124K5.4	cis	Stomach	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65737800-65748600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:65740800-65751400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:65744800-65748400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:65745000-65748400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:65745200-65748400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:65745200-65751200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:65745600-65749200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:65745600-65749200	Enhancers	HMEC	breast
9	chr7:65746400-65749200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:65746400-65749200	Enhancers	HSMMtube	muscle
11	chr7:65746600-65748400	Enhancers	Rectal Smooth Muscle	rectum
12	chr7:65746600-65748600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:65746600-65748800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr7:65746600-65749200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr7:65746600-65749200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:65746600-65749200	Enhancers	A549	lung
17	chr7:65746600-65749200	Enhancers	HSMM	muscle
18	chr7:65746600-65749200	Enhancers	HUVEC	blood vessel
19	chr7:65746600-65749200	Enhancers	NHLF	lung
20	chr7:65746800-65748400	Enhancers	Stomach Smooth Muscle	stomach
21	chr7:65746800-65748600	Enhancers	Adipose Nuclei	Adipose
22	chr7:65746800-65748600	Enhancers	HepG2	liver
23	chr7:65746800-65749000	Enhancers	Hela-S3	cervix
24	chr7:65746800-65749200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:65747200-65748400	Enhancers	NHDF-Ad	bronchial
26	chr7:65747200-65749000	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr7:65747200-65749200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:65747200-65749200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:65747200-65749200	Enhancers	NH-A	brain
30	chr7:65747200-65749200	Enhancers	Osteobl	bone
31	chr7:65747200-65754000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:65747600-65748800	Weak transcription	Brain Anterior Caudate	brain
33	chr7:65747600-65749400	Enhancers	NHEK	skin
34	chr7:65747800-65748800	Weak transcription	Colon Smooth Muscle	Colon
35	chr7:65747800-65766600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:65748000-65748800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:65748000-65751400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:65748200-65748400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr7:65748200-65748600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:65748200-65749000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr7:65748200-65749000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr7:65748200-65749000	Enhancers	Ovary	ovary
43	chr7:65748200-65749200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:65748200-65751200	Weak transcription	Aorta	Aorta

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