Variant report

Variant	rs778732
Chromosome Location	chr7:65822360-65822361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65821519..65823767-chr7:65824907..65826814,2	MCF-7	breast:
2	chr7:65578221..65580076-chr7:65821592..65823424,2	K562	blood:
3	chr7:65793897..65795825-chr7:65821186..65823238,2	K562	blood:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10246556	0.85[ASN][1000 genomes]
rs10247526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950032	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530490	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1267816	0.90[AFR][1000 genomes]
rs13222887	0.90[AFR][1000 genomes]
rs13224048	0.90[AFR][1000 genomes]
rs13232193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs13235972	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13237037	0.90[AFR][1000 genomes]
rs13237344	0.86[AFR][1000 genomes]
rs13241548	0.90[AFR][1000 genomes]
rs13242216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1392104	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1499614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546059	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1553174	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796228	0.90[AFR][1000 genomes]
rs1818045	0.88[ASN][1000 genomes]
rs1873494	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1979823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[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];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420170	0.80[EUR][1000 genomes]
rs2420171	0.85[EUR][1000 genomes]
rs2420172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2460425	0.85[EUR][1000 genomes]
rs2460426	0.85[EUR][1000 genomes]
rs2460431	0.85[EUR][1000 genomes]
rs2465120	0.83[EUR][1000 genomes]
rs316304	0.85[EUR][1000 genomes]
rs34192067	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34700450	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34807232	0.90[AFR][1000 genomes]
rs35823062	0.90[AFR][1000 genomes]
rs35825036	0.81[AFR][1000 genomes]
rs36104268	0.90[AFR][1000 genomes]
rs4145008	0.85[EUR][1000 genomes]
rs4149468	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236207	0.82[AMR][1000 genomes]
rs4481472	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718309	0.85[EUR][1000 genomes]
rs4718315	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718316	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718317	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718334	0.87[ASN][1000 genomes]
rs58668827	0.90[AFR][1000 genomes]
rs58669269	0.82[AFR][1000 genomes]
rs6460274	0.85[EUR][1000 genomes]
rs6460277	0.82[EUR][1000 genomes]
rs6460285	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6958289	0.82[AMR][1000 genomes];0.85[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];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959002	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6964245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6964530	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966322	0.85[EUR][1000 genomes]
rs6974723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs71563118	0.85[AFR][1000 genomes]
rs7778911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs778679	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778683	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778687	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778691	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778693	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778701	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778704	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778717	0.93[ASN][1000 genomes]
rs778718	0.87[AMR][1000 genomes]
rs7787230	0.85[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];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778733	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804223	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7808834	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs958550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs9769882	0.83[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs778732	VKORC1L1	cis	parietal	SCAN
rs778732	CRCP	cis	cerebellum	SCAN
rs778732	VKORC1L1	cis	Whole Blood	GTEx
rs778732	ZNF273	cis	parietal	SCAN
rs778732	CRCP	cis	parietal	SCAN
rs778732	ASL	cis	cerebellum	SCAN
rs778732	KIAA0564	trans	parietal	SCAN
rs778732	ZNF117	cis	parietal	SCAN
rs778732	GUSB	cis	Whole Blood	GTEx
rs778732	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778732	ZNF117	cis	cerebellum	SCAN
rs778732	ASL	cis	multi-tissue	Pritchard
rs778732	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs778732	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs778732	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:62 , 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	chr7:65814200-65823800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr7:65815000-65824600	Weak transcription	Lung	lung
5	chr7:65817000-65843400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:65817200-65824400	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:65817400-65823600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:65817400-65823800	Weak transcription	Spleen	Spleen
9	chr7:65817400-65824600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:65817400-65825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:65817400-65842600	Weak transcription	Gastric	stomach
12	chr7:65817600-65822400	Weak transcription	Stomach Mucosa	stomach
13	chr7:65817600-65823600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:65817600-65824600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:65817600-65826600	Weak transcription	Left Ventricle	heart
16	chr7:65817600-65828800	Weak transcription	Ovary	ovary
17	chr7:65817600-65842800	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:65817600-65843200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:65817600-65844200	Weak transcription	Right Atrium	heart
20	chr7:65817600-65844600	Weak transcription	Fetal Brain Female	brain
21	chr7:65818000-65843200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:65818400-65824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:65819200-65823400	Weak transcription	Liver	Liver
24	chr7:65819200-65844200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:65819400-65823400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:65819800-65826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr7:65820600-65822800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:65820600-65822800	Enhancers	Fetal Intestine Small	intestine
29	chr7:65820800-65822400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:65820800-65822800	Enhancers	HepG2	liver
31	chr7:65821000-65822400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:65821000-65822600	Enhancers	Duodenum Mucosa	Duodenum
33	chr7:65821000-65822800	Enhancers	Fetal Intestine Large	intestine
34	chr7:65821000-65822800	Flanking Active TSS	NHEK	skin
35	chr7:65821000-65824000	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:65821200-65822400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr7:65821200-65822600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:65821200-65822600	Strong transcription	Fetal Stomach	stomach
39	chr7:65821200-65822600	Flanking Active TSS	NH-A	brain
40	chr7:65821200-65825200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:65821400-65822400	Enhancers	Esophagus	oesophagus
42	chr7:65821400-65822600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:65821400-65823400	Active TSS	HMEC	breast
44	chr7:65821400-65824400	Weak transcription	Placenta	Placenta
45	chr7:65821400-65825600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:65821600-65822400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:65821600-65822400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:65821600-65822400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:65821600-65822400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:65821600-65822600	Strong transcription	Fetal Lung	lung

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