Variant report

Variant	rs778733
Chromosome Location	chr7:65820377-65820378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65819310..65820943-chr7:65826689..65828314,2	MCF-7	breast:
2	chr7:65819420..65821151-chr7:65824065..65825748,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10246556	0.85[ASN][1000 genomes]
rs10247526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807701	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807702	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950032	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530490	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1267816	0.82[AFR][1000 genomes]
rs13222887	0.82[AFR][1000 genomes]
rs13224048	0.82[AFR][1000 genomes]
rs13235972	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13237037	0.82[AFR][1000 genomes]
rs13241548	0.82[AFR][1000 genomes]
rs13242216	0.85[EUR][1000 genomes]
rs1392104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499613	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499614	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532573	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546059	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1553174	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796228	0.82[AFR][1000 genomes]
rs1818045	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1873494	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1979823	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420170	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2420171	0.91[EUR][1000 genomes]
rs2420172	0.91[EUR][1000 genomes]
rs2460425	0.91[EUR][1000 genomes]
rs2460426	0.91[EUR][1000 genomes]
rs2460431	0.91[EUR][1000 genomes]
rs2465120	0.88[EUR][1000 genomes]
rs316304	0.91[EUR][1000 genomes]
rs316317	0.85[EUR][1000 genomes]
rs316318	0.85[EUR][1000 genomes]
rs316321	0.85[EUR][1000 genomes]
rs316322	0.85[EUR][1000 genomes]
rs316325	0.85[EUR][1000 genomes]
rs316326	0.85[EUR][1000 genomes]
rs316327	0.85[EUR][1000 genomes]
rs316329	0.85[EUR][1000 genomes]
rs34192067	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34700450	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34807232	0.82[AFR][1000 genomes]
rs35823062	0.82[AFR][1000 genomes]
rs36104268	0.82[AFR][1000 genomes]
rs4145008	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4149468	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236207	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4481472	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4718309	0.91[EUR][1000 genomes]
rs4718315	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718316	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718317	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718333	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718334	0.87[ASN][1000 genomes]
rs58668827	0.82[AFR][1000 genomes]
rs6460274	0.91[EUR][1000 genomes]
rs6460277	0.87[EUR][1000 genomes]
rs6460285	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6958289	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6958420	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959002	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6964245	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6964530	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966322	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6974723	0.91[EUR][1000 genomes]
rs7778911	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs778679	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778683	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778687	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778691	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778693	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778701	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778704	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778717	0.93[ASN][1000 genomes]
rs778718	0.89[AMR][1000 genomes]
rs7787230	0.91[EUR][1000 genomes]
rs778729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778732	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804223	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7808834	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs958550	0.91[EUR][1000 genomes]
rs9769882	0.80[AMR][1000 genomes];0.88[EUR][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs778733	VKORC1L1	cis	Whole Blood	GTEx
rs778733	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs778733	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778733	GUSB	cis	Whole Blood	GTEx
rs778733	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs778733	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65805200-65843600	Weak transcription	Aorta	Aorta
2	chr7:65813400-65821200	Weak transcription	Fetal Stomach	stomach
3	chr7:65813800-65820600	Weak transcription	Fetal Intestine Small	intestine
4	chr7:65814000-65843800	Weak transcription	Brain Angular Gyrus	brain
5	chr7:65814200-65823800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr7:65815000-65824600	Weak transcription	Lung	lung
7	chr7:65817000-65821000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:65817200-65824400	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:65817400-65821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:65817400-65821600	Weak transcription	Fetal Lung	lung
12	chr7:65817400-65823600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:65817400-65823800	Weak transcription	Spleen	Spleen
14	chr7:65817400-65824600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:65817400-65825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:65817400-65842600	Weak transcription	Gastric	stomach
17	chr7:65817600-65820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:65817600-65820600	Weak transcription	NHDF-Ad	bronchial
19	chr7:65817600-65820800	Weak transcription	HepG2	liver
20	chr7:65817600-65820800	Weak transcription	NH-A	brain
21	chr7:65817600-65821000	Weak transcription	Fetal Intestine Large	intestine
22	chr7:65817600-65821000	Enhancers	HMEC	breast
23	chr7:65817600-65821200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:65817600-65821200	Weak transcription	HSMMtube	muscle
25	chr7:65817600-65821600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:65817600-65822400	Weak transcription	Stomach Mucosa	stomach
27	chr7:65817600-65823600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:65817600-65824600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr7:65817600-65826600	Weak transcription	Left Ventricle	heart
30	chr7:65817600-65828800	Weak transcription	Ovary	ovary
31	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
32	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
34	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
35	chr7:65817800-65821000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:65818000-65820800	Weak transcription	Osteobl	bone
37	chr7:65818000-65821000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:65818000-65821000	Weak transcription	NHLF	lung
39	chr7:65818000-65821200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:65818400-65824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr7:65818600-65820400	Enhancers	NHEK	skin
43	chr7:65818800-65820400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:65818800-65821000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:65819000-65820600	Weak transcription	Placenta	Placenta
46	chr7:65819000-65821400	Weak transcription	Esophagus	oesophagus
47	chr7:65819200-65823400	Weak transcription	Liver	Liver
48	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr7:65819400-65820800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:65819400-65820800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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