Variant report

Variant	rs9481047
Chromosome Location	chr6:110548383-110548384
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110525773..110528621-chr6:110547241..110549180,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11153226	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11751590	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11757055	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12110744	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12660791	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12662013	0.80[ASN][1000 genomes]
rs12665858	0.81[ASN][1000 genomes]
rs1462492	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1462493	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17071325	0.81[AMR][1000 genomes]
rs17071330	0.81[AMR][1000 genomes]
rs2334319	0.85[CEU][hapmap]
rs4257894	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4299857	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4339500	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4509164	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4945850	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4945851	0.86[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4947048	0.85[ASN][1000 genomes]
rs4947051	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4947058	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55649499	0.81[AMR][1000 genomes]
rs56122480	0.84[ASN][1000 genomes]
rs56135788	0.83[ASN][1000 genomes]
rs56287427	0.85[ASN][1000 genomes]
rs57983455	0.89[ASN][1000 genomes]
rs60495849	0.82[ASN][1000 genomes]
rs6568633	0.85[ASN][1000 genomes]
rs6568634	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6913554	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs6915379	0.82[ASN][1000 genomes]
rs6918148	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs6926540	0.87[ASN][1000 genomes]
rs6927667	0.85[ASN][1000 genomes]
rs6927697	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6927722	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6938106	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6938139	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6938653	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs719849	0.83[ASN][1000 genomes]
rs73535810	0.82[ASN][1000 genomes]
rs73535817	0.84[ASN][1000 genomes]
rs73535821	0.84[ASN][1000 genomes]
rs73535837	0.85[ASN][1000 genomes]
rs73535838	0.85[ASN][1000 genomes]
rs73537927	0.87[ASN][1000 genomes]
rs73537938	0.89[ASN][1000 genomes]
rs73537949	0.90[ASN][1000 genomes]
rs7744828	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7766850	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384735	0.84[ASN][1000 genomes]
rs9481045	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9481048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487318	0.93[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9487325	0.93[MEX][hapmap]
rs9487334	0.84[AMR][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	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1801843	chr6:110506109-110566328	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv949643	chr6:110537685-110889332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9481047	WASF1	cis	lymphoblastoid	seeQTL
rs9481047	FIG4	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110512200-110551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:110512200-110552200	Weak transcription	Right Ventricle	heart
3	chr6:110522400-110553200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:110527600-110551400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:110528000-110552800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:110528200-110557400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:110528600-110551400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:110528800-110551400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:110528800-110551400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:110528800-110551400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:110528800-110551600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:110528800-110551600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:110528800-110552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:110529000-110551400	Strong transcription	Primary B cells from cord blood	blood
15	chr6:110529400-110551400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:110530000-110556400	Weak transcription	Small Intestine	intestine
17	chr6:110530600-110551600	Strong transcription	Fetal Thymus	thymus
18	chr6:110530800-110558400	Weak transcription	Stomach Mucosa	stomach
19	chr6:110531400-110549400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:110531400-110552400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr6:110531800-110550800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:110532000-110551400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:110532800-110552000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:110534200-110550200	Weak transcription	A549	lung
25	chr6:110536000-110551400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr6:110537000-110548800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:110537400-110548400	Weak transcription	Fetal Heart	heart
28	chr6:110537400-110548600	Weak transcription	Brain Germinal Matrix	brain
29	chr6:110537400-110554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:110537800-110555000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:110537800-110558600	Weak transcription	Gastric	stomach
32	chr6:110538000-110548400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:110539000-110549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:110539000-110551400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:110539000-110554000	Weak transcription	Aorta	Aorta
36	chr6:110539000-110563600	Weak transcription	Lung	lung
37	chr6:110539000-110580200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:110539200-110552800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:110539200-110558200	Weak transcription	Brain Substantia Nigra	brain
40	chr6:110539200-110560000	Weak transcription	Esophagus	oesophagus
41	chr6:110539400-110548400	Weak transcription	NHEK	skin
42	chr6:110539400-110558400	Weak transcription	Fetal Brain Male	brain
43	chr6:110539400-110558600	Weak transcription	HUVEC	blood vessel
44	chr6:110540000-110567000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:110541200-110567200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:110541400-110548600	Weak transcription	K562	blood
47	chr6:110541400-110548800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:110541400-110550200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:110541400-110550200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:110541600-110555200	Weak transcription	HSMMtube	muscle

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