Variant report

Variant	rs4640889
Chromosome Location	chr6:56605332-56605333
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56593039..56595080-chr6:56605228..56607764,2	MCF-7	breast:

Extended variants
information (count: 182 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs10498811	0.83[EUR][1000 genomes]
rs10498812	0.81[CEU][hapmap]
rs10498813	0.81[CEU][hapmap]
rs11961141	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961342	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11966986	0.89[ASN][1000 genomes]
rs11967796	0.89[ASN][1000 genomes]
rs11968575	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970648	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190784	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191164	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192567	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194625	0.81[CEU][hapmap]
rs13194904	0.81[CEU][hapmap]
rs13196211	0.82[EUR][1000 genomes]
rs13198399	0.99[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13200166	0.81[CEU][hapmap]
rs13203000	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13203681	0.81[CEU][hapmap]
rs13204466	0.81[CEU][hapmap]
rs13205013	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13205667	0.81[CEU][hapmap]
rs13206849	0.83[EUR][1000 genomes]
rs13207768	0.81[CEU][hapmap]
rs13208409	0.82[EUR][1000 genomes]
rs13210876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213878	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217390	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13218913	0.81[CEU][hapmap]
rs13219546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs13220618	0.81[CEU][hapmap]
rs13220628	0.86[CEU][hapmap]
rs16888070	0.89[ASN][1000 genomes]
rs16888096	0.89[ASN][1000 genomes]
rs16888106	0.89[ASN][1000 genomes]
rs16888118	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888124	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888126	0.80[EUR][1000 genomes]
rs16888128	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888130	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888133	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888171	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17684748	0.81[CEU][hapmap]
rs17684772	0.81[CEU][hapmap]
rs17684784	0.81[CEU][hapmap]
rs17684802	0.81[CEU][hapmap]
rs17684878	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs17684884	0.81[CEU][hapmap]
rs17751682	0.85[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs17751695	0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs17751977	0.81[CEU][hapmap]
rs17752046	0.81[CEU][hapmap]
rs17752106	0.81[CEU][hapmap]
rs1903332	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2144407	0.89[ASN][1000 genomes]
rs2180148	0.89[ASN][1000 genomes]
rs2207678	0.89[ASN][1000 genomes]
rs2967960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967963	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002003	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002004	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002007	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002009	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3002010	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002011	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34429594	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34455199	1.00[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	1.00[EUR][1000 genomes]
rs34566275	1.00[EUR][1000 genomes]
rs34576803	0.81[EUR][1000 genomes]
rs34587484	1.00[EUR][1000 genomes]
rs34623351	1.00[EUR][1000 genomes]
rs34703847	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34724718	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34803237	1.00[EUR][1000 genomes]
rs34812826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824960	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832779	0.99[EUR][1000 genomes]
rs35089136	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206656	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35326806	0.97[EUR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35494794	0.97[EUR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35876418	1.00[EUR][1000 genomes]
rs35920751	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36068365	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4072271	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073960	0.82[AFR][1000 genomes]
rs4074101	0.85[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.80[EUR][1000 genomes]
rs41267673	0.89[ASN][1000 genomes]
rs41267675	1.00[EUR][1000 genomes]
rs41271876	0.89[ASN][1000 genomes]
rs41271878	0.89[ASN][1000 genomes]
rs4133076	0.89[ASN][1000 genomes]
rs4275049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299824	0.81[CEU][hapmap]
rs4348308	0.81[CEU][hapmap]
rs4371846	0.81[CEU][hapmap]
rs4415160	0.81[CEU][hapmap]
rs4457154	0.81[CEU][hapmap]
rs45553042	0.89[ASN][1000 genomes]
rs4574644	1.00[ASN][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56094263	1.00[ASN][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs56196625	0.89[ASN][1000 genomes]
rs57289287	0.89[ASN][1000 genomes]
rs57350484	0.89[ASN][1000 genomes]
rs57392123	0.89[ASN][1000 genomes]
rs57488435	0.89[ASN][1000 genomes]
rs58565063	0.89[ASN][1000 genomes]
rs59073430	0.89[ASN][1000 genomes]
rs59085778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59162324	1.00[ASN][1000 genomes]
rs59247267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59772940	0.89[ASN][1000 genomes]
rs59889120	0.89[ASN][1000 genomes]
rs60360551	0.89[ASN][1000 genomes]
rs60498201	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412526	0.83[EUR][1000 genomes]
rs62412528	0.83[EUR][1000 genomes]
rs62412531	0.83[EUR][1000 genomes]
rs62412532	0.83[EUR][1000 genomes]
rs62412544	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412556	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6459167	0.89[ASN][1000 genomes]
rs6459168	0.89[ASN][1000 genomes]
rs6900572	0.89[ASN][1000 genomes]
rs6901176	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903815	0.89[ASN][1000 genomes]
rs6904535	0.83[AMR][1000 genomes]
rs6905603	0.81[CEU][hapmap]
rs6916813	0.89[ASN][1000 genomes]
rs6918949	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs6924375	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926134	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934714	0.81[CEU][hapmap]
rs6938003	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941626	0.89[ASN][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs73746926	0.89[ASN][1000 genomes]
rs73746929	0.89[ASN][1000 genomes]
rs73746930	0.89[ASN][1000 genomes]
rs73746931	0.89[ASN][1000 genomes]
rs7749100	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs7749437	0.89[ASN][1000 genomes]
rs7758867	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7759479	0.89[ASN][1000 genomes]
rs7760503	0.89[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs7761027	0.89[ASN][1000 genomes]
rs7761501	0.81[CEU][hapmap]
rs7761729	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs7767128	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7771085	0.80[CEU][hapmap]
rs7775134	1.00[CHD][hapmap];0.89[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4640889	RAB23	cis	multi-tissue	Pritchard
rs4640889	BMP5	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:56590200-56607000	Weak transcription	Pancreas	Pancrea
3	chr6:56592800-56606000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:56592800-56606800	Weak transcription	Aorta	Aorta
5	chr6:56592800-56611800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:56593400-56605400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:56593400-56606800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:56594800-56607000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:56596400-56606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:56596400-56606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:56596400-56606800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:56597400-56606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:56597800-56606000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:56598000-56606600	Weak transcription	Fetal Stomach	stomach
16	chr6:56598000-56607000	Weak transcription	Gastric	stomach
17	chr6:56598400-56606600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:56598400-56607000	Weak transcription	HUVEC	blood vessel
19	chr6:56599400-56607200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:56600600-56606000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:56600600-56606800	Weak transcription	NHDF-Ad	bronchial
22	chr6:56602200-56607000	Enhancers	Brain Hippocampus Middle	brain
23	chr6:56603000-56606200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:56603400-56605600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:56603400-56605600	Enhancers	Left Ventricle	heart
26	chr6:56603400-56607000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr6:56603600-56606800	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:56603600-56606800	Enhancers	Brain Substantia Nigra	brain
29	chr6:56604000-56606800	Enhancers	Brain Angular Gyrus	brain
30	chr6:56604200-56605400	Enhancers	Right Atrium	heart
31	chr6:56604200-56605400	Enhancers	Right Ventricle	heart
32	chr6:56604200-56606000	Enhancers	Colon Smooth Muscle	Colon
33	chr6:56604400-56605400	Enhancers	Stomach Mucosa	stomach
34	chr6:56604600-56605600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:56604600-56606200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:56604600-56606600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:56604600-56608400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:56604800-56605600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:56604800-56605600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:56604800-56605600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:56604800-56605600	Flanking Active TSS	Liver	Liver
42	chr6:56604800-56605600	Enhancers	Spleen	Spleen
43	chr6:56604800-56605600	Enhancers	NH-A	brain
44	chr6:56604800-56605800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:56604800-56606000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:56604800-56606800	Enhancers	Brain Anterior Caudate	brain
47	chr6:56604800-56608400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr6:56604800-56610000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr6:56605000-56605400	Enhancers	Adipose Nuclei	Adipose
50	chr6:56605000-56605400	Enhancers	Fetal Intestine Large	intestine

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