Variant report

Variant	rs778728
Chromosome Location	chr7:65826462-65826463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65821519..65823767-chr7:65824907..65826814,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1000464	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1002053	0.83[AMR][1000 genomes]
rs10224872	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10228885	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10240949	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10250544	0.89[EUR][1000 genomes]
rs10255397	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10256544	0.91[EUR][1000 genomes]
rs10257911	0.87[EUR][1000 genomes]
rs10260426	0.90[EUR][1000 genomes]
rs10261398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10263690	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10276077	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10282433	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10447522	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10807704	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1083554	0.85[EUR][1000 genomes]
rs10950033	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11760844	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11764589	0.84[EUR][1000 genomes]
rs11765965	0.84[AMR][1000 genomes]
rs11769079	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11984115	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12531677	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534500	0.85[EUR][1000 genomes]
rs12537823	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13225672	0.82[EUR][1000 genomes]
rs13230545	0.90[EUR][1000 genomes]
rs13309935	0.90[EUR][1000 genomes]
rs1532571	0.90[EUR][1000 genomes]
rs1643375	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1695815	0.84[AMR][1000 genomes]
rs1695820	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1875057	0.90[EUR][1000 genomes]
rs2036263	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2036264	0.83[AMR][1000 genomes]
rs2088653	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2088655	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2420173	0.81[EUR][1000 genomes]
rs2420174	0.81[EUR][1000 genomes]
rs2420608	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28491091	0.86[EUR][1000 genomes]
rs2901152	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2901155	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2909688	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34913718	0.82[EUR][1000 genomes]
rs3893216	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3935391	0.81[AMR][1000 genomes]
rs4078376	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4149461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236208	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4587224	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4623294	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718319	0.80[EUR][1000 genomes]
rs4718324	0.83[EUR][1000 genomes]
rs4718328	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4718329	0.84[EUR][1000 genomes]
rs4718330	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55748098	0.81[AMR][1000 genomes]
rs6460278	0.86[EUR][1000 genomes]
rs6460279	0.86[EUR][1000 genomes]
rs6460282	0.87[EUR][1000 genomes]
rs6460284	0.90[EUR][1000 genomes]
rs6460287	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6460290	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460291	0.81[AMR][1000 genomes]
rs6460292	0.83[AMR][1000 genomes]
rs6460293	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6460302	0.81[EUR][1000 genomes]
rs6944374	0.87[EUR][1000 genomes]
rs6951503	0.90[EUR][1000 genomes]
rs6952182	0.87[EUR][1000 genomes]
rs6952473	0.83[EUR][1000 genomes]
rs6958294	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6959268	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6960446	0.90[EUR][1000 genomes]
rs6962717	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6963228	0.82[EUR][1000 genomes]
rs6964437	0.87[EUR][1000 genomes]
rs6967708	0.81[EUR][1000 genomes]
rs6971752	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6974614	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6976714	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6978028	0.83[EUR][1000 genomes]
rs6979452	0.91[EUR][1000 genomes]
rs6980451	0.80[EUR][1000 genomes]
rs709595	0.83[AMR][1000 genomes]
rs709596	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs709597	0.83[AMR][1000 genomes]
rs71526537	0.82[EUR][1000 genomes]
rs7778322	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7781880	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7782704	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7782806	0.81[EUR][1000 genomes]
rs7783613	0.83[AMR][1000 genomes]
rs7783779	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs778680	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778682	0.83[AMR][1000 genomes]
rs778684	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778685	0.84[AMR][1000 genomes]
rs778686	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778689	0.85[AMR][1000 genomes]
rs778690	0.83[EUR][1000 genomes]
rs778697	0.83[EUR][1000 genomes]
rs778702	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs778703	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778705	0.84[EUR][1000 genomes]
rs778707	0.84[EUR][1000 genomes]
rs778711	0.84[EUR][1000 genomes]
rs778715	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778716	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778719	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs778720	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778723	0.83[AMR][1000 genomes]
rs778724	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778726	0.84[AMR][1000 genomes]
rs778734	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778735	0.82[AMR][1000 genomes]
rs778736	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7787482	0.83[EUR][1000 genomes]
rs7789615	0.80[EUR][1000 genomes]
rs7796162	0.88[EUR][1000 genomes]
rs7798630	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs809025	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs880166	0.90[EUR][1000 genomes]
rs937495	0.81[AMR][1000 genomes]
rs949930	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9969301	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs778728	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs778728	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs778728	LINC00174	cis	Thyroid	GTEx
rs778728	RP4-756H11.3	cis	lung	GTEx
rs778728	RP4-756H11.3	cis	Thyroid	GTEx
rs778728	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs778728	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs778728	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778728	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs778728	RNU6-96P	cis	Thyroid	GTEx
rs778728	RP4-756H11.3	cis	Artery Tibial	GTEx
rs778728	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs778728	GTF2IRD1P1	cis	Thyroid	GTEx
rs778728	RP4-756H11.3	cis	Artery Aorta	GTEx
rs778728	GS1-124K5.4	cis	Stomach	GTEx
rs778728	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs778728	GS1-124K5.2	cis	Whole Blood	GTEx
rs778728	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs778728	GS1-124K5.11	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65805200-65843600	Weak transcription	Aorta	Aorta
2	chr7:65814000-65843800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:65817400-65842600	Weak transcription	Gastric	stomach
5	chr7:65817600-65826600	Weak transcription	Left Ventricle	heart
6	chr7:65817600-65828800	Weak transcription	Ovary	ovary
7	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
10	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
11	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:65822000-65831800	Weak transcription	HSMM	muscle
14	chr7:65822000-65843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:65822200-65828800	Weak transcription	Osteobl	bone
16	chr7:65822400-65831400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:65822400-65831400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:65822600-65827400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:65822800-65839200	Weak transcription	Fetal Intestine Small	intestine
20	chr7:65822800-65841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:65823400-65843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:65824000-65831200	Weak transcription	Fetal Lung	lung
23	chr7:65824600-65826600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:65824800-65827400	Weak transcription	HepG2	liver
25	chr7:65824800-65843600	Weak transcription	Esophagus	oesophagus
26	chr7:65825000-65826800	Strong transcription	Fetal Stomach	stomach
27	chr7:65825000-65828800	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:65825000-65833800	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:65825000-65844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:65825200-65826600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:65825200-65826800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:65825200-65827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:65825200-65827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:65825200-65827400	Weak transcription	Lung	lung
35	chr7:65825200-65831200	Weak transcription	NHDF-Ad	bronchial
36	chr7:65825200-65841200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:65825200-65841200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:65825200-65842200	Weak transcription	Spleen	Spleen
39	chr7:65825200-65844200	Weak transcription	NHLF	lung
40	chr7:65826000-65826800	Enhancers	Placenta	Placenta
41	chr7:65826200-65827000	Enhancers	NHEK	skin
42	chr7:65826200-65842600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:65826400-65826600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:65826400-65826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:65826400-65829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:65826400-65842400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:65826400-65842800	Weak transcription	Liver	Liver

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