Variant report

Variant	rs12530490
Chromosome Location	chr7:65691647-65691648
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	chr7:65680452..65683306-chr7:65691052..65694234,3	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10247526	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10807701	1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10807702	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10950032	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12667373	0.83[AMR][1000 genomes]
rs13235972	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13242216	0.85[EUR][1000 genomes]
rs13308751	0.81[AFR][1000 genomes]
rs1392104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1499613	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1499614	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1532573	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1546059	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1553174	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs160637	1.00[YRI][hapmap]
rs160643	1.00[YRI][hapmap]
rs160646	1.00[YRI][hapmap]
rs160652	1.00[YRI][hapmap]
rs186378	0.81[AFR][1000 genomes]
rs1873494	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979823	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2243480	1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2257790	0.81[ASN][1000 genomes]
rs2420170	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420171	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2420172	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460422	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2460425	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2460426	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2460431	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465120	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs313803	1.00[YRI][hapmap]
rs313819	0.81[AFR][1000 genomes]
rs313822	0.81[AFR][1000 genomes]
rs313831	1.00[YRI][hapmap]
rs316304	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs316314	1.00[YRI][hapmap]
rs316315	1.00[YRI][hapmap]
rs316317	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs316318	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs316321	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs316322	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs316325	0.85[EUR][1000 genomes]
rs316326	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs316327	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs316329	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs316331	1.00[YRI][hapmap]
rs316334	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34192067	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34700450	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs383402	1.00[YRI][hapmap]
rs4145008	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4149468	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs419603	1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs422164	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4236207	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs431076	0.81[ASN][1000 genomes]
rs4481472	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718309	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718315	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718316	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718317	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718333	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6460274	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6460277	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460285	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6958289	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6958420	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6959002	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6964245	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6964530	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6966322	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6974723	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7778911	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778679	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778683	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778687	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778691	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs778693	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs778701	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs778704	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs778717	0.81[ASN][1000 genomes]
rs778718	0.80[AMR][1000 genomes]
rs7787230	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778729	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778732	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs778733	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792391	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7804223	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7808834	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958550	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9769882	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12530490	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12530490	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs12530490	VKORC1L1	cis	Whole Blood	GTEx
rs12530490	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs12530490	RP4-756H11.3	cis	lung	GTEx
rs12530490	GUSB	cis	Whole Blood	GTEx
rs12530490	ASL	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65676000-65696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
4	chr7:65676200-65696200	Weak transcription	Fetal Stomach	stomach
5	chr7:65676600-65693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:65677000-65694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:65677200-65693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:65685600-65696200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:65686800-65701600	Weak transcription	Osteobl	bone
10	chr7:65686800-65715400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:65687000-65701800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:65687000-65701800	Weak transcription	NHDF-Ad	bronchial
13	chr7:65687800-65701800	Weak transcription	Spleen	Spleen
14	chr7:65687800-65703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:65689400-65703600	Weak transcription	NHLF	lung
16	chr7:65689600-65695800	Weak transcription	Brain Substantia Nigra	brain
17	chr7:65689600-65696200	Weak transcription	Lung	lung
18	chr7:65689600-65697800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:65689600-65701800	Weak transcription	Gastric	stomach
20	chr7:65689600-65715800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:65689800-65695000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:65689800-65695600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:65689800-65696200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:65689800-65697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:65689800-65701800	Weak transcription	Fetal Lung	lung
26	chr7:65689800-65701800	Weak transcription	HMEC	breast
27	chr7:65689800-65702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:65690000-65694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65690000-65698400	Weak transcription	Liver	Liver
30	chr7:65690200-65701800	Weak transcription	Ovary	ovary
31	chr7:65691200-65700200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:65691400-65692600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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