Variant report

Variant	rs4415160
Chromosome Location	chr6:56686222-56686223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56681788..56686240-chr6:56707672..56709925,4	MCF-7	breast:
2	chr6:56685654..56687810-chr6:56707854..56710346,2	MCF-7	breast:
3	chr6:56674708..56676996-chr6:56685905..56688829,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10498812	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11756551	0.88[EUR][1000 genomes]
rs11968575	0.81[CEU][hapmap]
rs11970648	1.00[CEU][hapmap]
rs13190784	0.89[MEX][hapmap]
rs13190854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13192540	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13192931	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13195601	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198204	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13198597	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13200166	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13200559	0.86[EUR][1000 genomes]
rs13200768	0.90[EUR][1000 genomes]
rs13200868	0.84[EUR][1000 genomes]
rs13201639	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13201733	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap]
rs13203148	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203327	0.87[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13208409	0.83[EUR][1000 genomes]
rs13211879	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13214893	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap]
rs13218913	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13220618	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220851	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1610156	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1610157	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16888171	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs16888184	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17684730	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17684784	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs17684802	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17684878	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17684941	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751682	0.89[MEX][hapmap]
rs17751695	0.89[MEX][hapmap]
rs17751966	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17752002	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17752213	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28360570	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap]
rs3002011	0.80[CEU][hapmap]
rs34083827	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34171958	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34228698	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34359353	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34425815	0.91[EUR][1000 genomes]
rs34500949	0.86[EUR][1000 genomes]
rs34520435	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34612783	0.90[EUR][1000 genomes]
rs34614087	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34640766	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34866877	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34896026	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34966024	0.85[EUR][1000 genomes]
rs35073881	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35080938	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35081015	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35225175	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35242294	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35251663	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35407078	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35439100	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35440408	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35440822	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35461301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35566812	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35609883	0.91[EUR][1000 genomes]
rs35642890	0.91[EUR][1000 genomes]
rs35696739	0.91[EUR][1000 genomes]
rs35828379	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35851452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35873865	0.89[EUR][1000 genomes]
rs35886823	0.91[EUR][1000 genomes]
rs35986172	0.83[EUR][1000 genomes]
rs36022925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36037734	0.91[EUR][1000 genomes]
rs36094082	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4074101	0.89[MEX][hapmap]
rs4299824	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4532444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs56037312	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56368885	0.85[EUR][1000 genomes]
rs58980183	0.85[EUR][1000 genomes]
rs59432342	0.91[EUR][1000 genomes]
rs61601344	0.91[EUR][1000 genomes]
rs62411366	0.84[EUR][1000 genomes]
rs62411367	0.86[EUR][1000 genomes]
rs62411372	0.90[EUR][1000 genomes]
rs62411375	0.91[EUR][1000 genomes]
rs62411376	0.91[EUR][1000 genomes]
rs6904535	0.86[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6910414	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6914293	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6918949	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6928104	0.84[EUR][1000 genomes]
rs6930172	0.82[AFR][1000 genomes]
rs6934714	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71564854	0.91[EUR][1000 genomes]
rs71564855	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564856	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71564861	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71564863	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7758867	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7761501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7766565	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7775182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1034418	chr6:56651245-56700449	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4415160	RAB23	cis	multi-tissue	Pritchard
rs4415160	DST	cis	cerebellum	SCAN
rs4415160	BMP5	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56674200-56692400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:56674200-56703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:56674600-56686400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:56679200-56687400	Enhancers	Brain Substantia Nigra	brain
5	chr6:56679800-56693400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:56679800-56693400	Weak transcription	NH-A	brain
7	chr6:56680000-56689000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:56680600-56690400	Weak transcription	HSMMtube	muscle
9	chr6:56681400-56692600	Weak transcription	Osteobl	bone
10	chr6:56681400-56702200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:56681400-56702200	Weak transcription	NHDF-Ad	bronchial
12	chr6:56681600-56702400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:56683000-56692600	Weak transcription	Right Ventricle	heart
14	chr6:56683600-56687200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:56684000-56689200	Weak transcription	HUVEC	blood vessel
16	chr6:56684000-56690600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:56684000-56703800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:56684200-56686400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:56684200-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:56684600-56686400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:56684600-56686800	Enhancers	Brain Hippocampus Middle	brain
22	chr6:56684600-56687400	Enhancers	Brain Anterior Caudate	brain
23	chr6:56684800-56686400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:56684800-56686600	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:56684800-56686600	Enhancers	Fetal Heart	heart
26	chr6:56684800-56686600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:56684800-56687200	Enhancers	Brain Angular Gyrus	brain
28	chr6:56684800-56687200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:56684800-56687200	Enhancers	A549	lung
30	chr6:56685000-56686800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr6:56685200-56690400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:56685400-56686400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:56685400-56687400	Enhancers	Psoas Muscle	Psoas
34	chr6:56685600-56686400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:56685600-56686800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:56685600-56687200	Enhancers	Colon Smooth Muscle	Colon
37	chr6:56685600-56700000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:56686000-56686400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:56686000-56686400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr6:56686000-56686400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:56686000-56686400	Enhancers	Fetal Stomach	stomach
42	chr6:56686000-56686400	Enhancers	Left Ventricle	heart
43	chr6:56686200-56686400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:56686200-56686400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:56686200-56686400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:56686200-56687000	Weak transcription	NHLF	lung
47	chr6:56686200-56687400	Enhancers	GM12878-XiMat	blood
48	chr6:56686200-56689200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:56686200-56690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:56686200-56690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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