Variant report

Variant	rs778679
Chromosome Location	chr7:65840911-65840912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10246556	0.81[ASN][1000 genomes]
rs10247526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10950032	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530490	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1267816	0.91[AFR][1000 genomes]
rs1267819	0.91[AFR][1000 genomes]
rs1267820	0.91[AFR][1000 genomes]
rs13222887	0.91[AFR][1000 genomes]
rs13224048	0.91[AFR][1000 genomes]
rs13232193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs13235972	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13237037	0.91[AFR][1000 genomes]
rs13237344	0.87[AFR][1000 genomes]
rs13241548	0.91[AFR][1000 genomes]
rs13242216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs1392104	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1499613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[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];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1499614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1532573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1546059	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1553174	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796220	0.91[AFR][1000 genomes]
rs1796228	0.91[AFR][1000 genomes]
rs1818045	0.84[ASN][1000 genomes]
rs1873494	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1979823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[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];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2420170	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2420171	0.88[EUR][1000 genomes]
rs2420172	0.88[EUR][1000 genomes]
rs2460425	0.88[EUR][1000 genomes]
rs2460426	0.88[EUR][1000 genomes]
rs2460431	0.88[EUR][1000 genomes]
rs2465120	0.85[EUR][1000 genomes]
rs2533288	0.87[AFR][1000 genomes]
rs2707831	0.91[AFR][1000 genomes]
rs2707844	0.87[AFR][1000 genomes]
rs316304	0.88[EUR][1000 genomes]
rs316317	0.82[EUR][1000 genomes]
rs316318	0.82[EUR][1000 genomes]
rs316321	0.82[EUR][1000 genomes]
rs316322	0.82[EUR][1000 genomes]
rs316325	0.82[EUR][1000 genomes]
rs316326	0.82[EUR][1000 genomes]
rs316327	0.82[EUR][1000 genomes]
rs316329	0.82[EUR][1000 genomes]
rs34192067	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34363376	0.82[EUR][1000 genomes]
rs34700450	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34807232	0.91[AFR][1000 genomes]
rs35823062	0.91[AFR][1000 genomes]
rs35825036	0.82[AFR][1000 genomes]
rs36104268	0.91[AFR][1000 genomes]
rs4145008	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4149468	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236207	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4481472	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4718309	0.88[EUR][1000 genomes]
rs4718315	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718316	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718317	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718334	0.83[ASN][1000 genomes]
rs58668827	0.91[AFR][1000 genomes]
rs58669269	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6460274	0.88[EUR][1000 genomes]
rs6460277	0.84[EUR][1000 genomes]
rs6460285	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6958289	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6958420	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6959002	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6964245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6964530	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966322	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6974723	0.88[EUR][1000 genomes]
rs71563118	0.86[AFR][1000 genomes]
rs7778911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778687	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778691	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778693	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778698	0.84[ASN][1000 genomes]
rs778701	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778704	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778717	0.98[ASN][1000 genomes]
rs778718	0.91[AMR][1000 genomes]
rs7787230	0.88[EUR][1000 genomes]
rs778729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778733	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7804223	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7808834	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs958550	0.88[EUR][1000 genomes]
rs9769882	0.82[AMR][1000 genomes];0.85[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	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
5	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
6	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs778679	VKORC1L1	cis	parietal	SCAN
rs778679	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778679	VKORC1L1	cis	Whole Blood	GTEx
rs778679	RP4-756H11.3	cis	lung	GTEx
rs778679	ASL	cis	multi-tissue	Pritchard
rs778679	ZNF117	cis	cerebellum	SCAN
rs778679	GUSB	cis	Whole Blood	GTEx
rs778679	ZNF273	cis	parietal	SCAN
rs778679	CRCP	cis	parietal	SCAN
rs778679	CRCP	cis	cerebellum	SCAN
rs778679	ZNF117	cis	parietal	SCAN
rs778679	ASL	cis	cerebellum	SCAN
rs778679	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs778679	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

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	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
6	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
8	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
9	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:65822000-65843800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:65822800-65841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:65823400-65843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:65824800-65843600	Weak transcription	Esophagus	oesophagus
15	chr7:65825000-65844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:65825200-65841200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:65825200-65841200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:65825200-65842200	Weak transcription	Spleen	Spleen
19	chr7:65825200-65844200	Weak transcription	NHLF	lung
20	chr7:65826200-65842600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:65826400-65842400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:65826400-65842800	Weak transcription	Liver	Liver
23	chr7:65826600-65841200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:65827000-65843800	Weak transcription	NHEK	skin
25	chr7:65827400-65841200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:65831400-65841200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:65831600-65841200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:65831800-65844200	Weak transcription	NHDF-Ad	bronchial
29	chr7:65832000-65841200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:65832000-65843200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:65832000-65844200	Weak transcription	Fetal Lung	lung
32	chr7:65833800-65842600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:65836200-65841400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:65836400-65843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:65836600-65841800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:65836600-65846400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:65838200-65842600	Weak transcription	Pancreas	Pancrea
38	chr7:65838400-65843400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:65838800-65844600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:65839000-65844000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:65839000-65844000	Weak transcription	Placenta	Placenta
42	chr7:65839000-65844800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:65839200-65842200	Weak transcription	Lung	lung
44	chr7:65839200-65843800	Weak transcription	Adipose Nuclei	Adipose
45	chr7:65839400-65842600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:65839400-65843800	Weak transcription	Ovary	ovary
47	chr7:65839400-65844400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:65839400-65844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:65839600-65843800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:65839800-65841400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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