Variant report

Variant	rs7009781
Chromosome Location	chr8:54873211-54873212
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	chr8:54866574..54869631-chr8:54872267..54874900,3	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10101097	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10113246	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1039926	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs10504161	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs1050523	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958396	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10958397	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11783652	0.82[CHB][hapmap]
rs11986577	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11991952	0.87[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap]
rs11993367	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11993959	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs11994629	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs11996666	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11997954	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12056381	0.99[ASN][1000 genomes]
rs12114043	0.81[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs12674671	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12676510	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12677696	0.88[EUR][1000 genomes]
rs12679542	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs16919699	0.80[CHB][hapmap]
rs16919782	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs16919784	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs1828835	0.84[ASN][1000 genomes]
rs2037068	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271567	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2292590	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2375697	0.97[ASN][1000 genomes]
rs28494618	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4506187	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4515510	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4737457	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4737479	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs4737485	0.81[ASN][1000 genomes]
rs4737486	0.84[ASN][1000 genomes]
rs4737487	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs4737488	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4738519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4738544	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4738556	0.99[ASN][1000 genomes]
rs4738564	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4738586	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57872947	0.90[ASN][1000 genomes]
rs58387069	0.84[ASN][1000 genomes]
rs58419852	0.84[ASN][1000 genomes]
rs58929175	0.99[ASN][1000 genomes]
rs58948369	0.84[ASN][1000 genomes]
rs59882028	0.97[ASN][1000 genomes]
rs60183530	0.84[ASN][1000 genomes]
rs61271559	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61319412	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6473900	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6473909	0.82[ASN][1000 genomes]
rs6473911	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs6473914	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs6473915	0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs6983694	0.84[ASN][1000 genomes]
rs7011379	0.84[ASN][1000 genomes]
rs7012031	0.93[ASW][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs72614663	1.00[ASN][1000 genomes]
rs72614664	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72614665	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72614666	0.84[ASN][1000 genomes]
rs72614667	0.84[ASN][1000 genomes]
rs72614668	0.83[ASN][1000 genomes]
rs7463083	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7463261	0.97[ASN][1000 genomes]
rs7464767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7815216	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7842911	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap]
rs9298497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs952194	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]
rs9643823	0.99[ASN][1000 genomes]
rs9643824	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2758160	chr8:54832990-55016965	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759617	chr8:54832990-55016965	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv427821	chr8:54832990-55016965	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7009781	MRPL15	Cis_1M	lymphoblastoid	RTeQTL
rs7009781	MRPL15	cis	lymphoblastoid	seeQTL
rs7009781	MRPL15	cis	cerebellum	SCAN
rs7009781	TCEA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54856400-54889400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr8:54858200-54879000	Weak transcription	Right Atrium	heart
3	chr8:54859600-54881200	Weak transcription	Hela-S3	cervix
4	chr8:54859600-54885400	Weak transcription	K562	blood
5	chr8:54862000-54879200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:54862200-54879200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:54866600-54873400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr8:54866600-54893600	Weak transcription	Fetal Kidney	kidney
9	chr8:54866800-54875400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr8:54866800-54885200	Weak transcription	NH-A	brain
11	chr8:54866800-54898000	Weak transcription	Colon Smooth Muscle	Colon
12	chr8:54866800-54898200	Weak transcription	Fetal Heart	heart
13	chr8:54867000-54874200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:54867000-54875600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr8:54867000-54884800	Weak transcription	HUVEC	blood vessel
16	chr8:54867600-54876000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:54867600-54877400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr8:54867800-54875200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:54867800-54876600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:54868200-54895600	Weak transcription	Brain Angular Gyrus	brain
21	chr8:54868400-54874400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:54868600-54873800	Strong transcription	NHLF	lung
23	chr8:54868800-54874400	Strong transcription	A549	lung
24	chr8:54870400-54873800	Strong transcription	Placenta	Placenta
25	chr8:54870400-54875200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr8:54870400-54875600	Weak transcription	HepG2	liver
27	chr8:54870400-54875600	Weak transcription	HMEC	breast
28	chr8:54870600-54874600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:54870600-54879400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:54870800-54874200	Strong transcription	Brain Anterior Caudate	brain
31	chr8:54870800-54874400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:54870800-54874800	Strong transcription	Fetal Muscle Leg	muscle
33	chr8:54870800-54879200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:54871000-54878000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr8:54871000-54879200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr8:54871200-54875200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:54871400-54873600	Strong transcription	NHDF-Ad	bronchial
38	chr8:54871400-54873800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:54871400-54874400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr8:54871400-54874400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:54871400-54874600	Strong transcription	Primary B cells from cord blood	blood
42	chr8:54871400-54891000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr8:54871400-54898000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr8:54871600-54873800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr8:54871600-54877400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr8:54871600-54932600	Weak transcription	Fetal Brain Male	brain
47	chr8:54871800-54873800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr8:54871800-54879200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:54871800-54880800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:54872000-54873600	Strong transcription	Brain Inferior Temporal Lobe	brain

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