Variant report

Variant	rs1903332
Chromosome Location	chr6:56722235-56722236
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56714030..56717677-chr6:56722118..56725337,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10498812	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10498813	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs11756551	0.81[EUR][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11970648	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13190784	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs13190854	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13191826	1.00[ASN][1000 genomes]
rs13192540	0.95[EUR][1000 genomes]
rs13192931	0.95[EUR][1000 genomes]
rs13194625	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs13194904	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs13195601	0.92[EUR][1000 genomes]
rs13198204	0.85[EUR][1000 genomes]
rs13198597	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13200166	0.94[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13200768	0.83[EUR][1000 genomes]
rs13200868	1.00[ASN][1000 genomes]
rs13201639	0.85[EUR][1000 genomes]
rs13201733	0.85[EUR][1000 genomes]
rs13203148	0.91[EUR][1000 genomes]
rs13203327	0.81[EUR][1000 genomes]
rs13203681	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13204466	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs13205667	0.94[CEU][hapmap]
rs13207768	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs13209099	0.80[CEU][hapmap]
rs13211879	0.89[EUR][1000 genomes]
rs13214893	0.98[EUR][1000 genomes]
rs13215883	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13218913	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13220618	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs13220628	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs13220851	0.86[EUR][1000 genomes]
rs1610156	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1610157	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16888171	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs16888184	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888186	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888189	0.80[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs16888192	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17684730	0.85[EUR][1000 genomes]
rs17684748	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs17684772	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs17684784	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs17684802	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs17684878	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17684884	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17684941	0.98[EUR][1000 genomes]
rs17751966	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs17751977	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs17752002	0.85[EUR][1000 genomes]
rs17752046	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs17752106	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17752213	0.98[EUR][1000 genomes]
rs28360570	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002010	1.00[CHB][hapmap]
rs3002011	1.00[CHB][hapmap]
rs34083827	0.97[EUR][1000 genomes]
rs34171958	0.85[EUR][1000 genomes]
rs34228698	0.85[EUR][1000 genomes]
rs34359353	0.85[EUR][1000 genomes]
rs34425815	0.84[EUR][1000 genomes]
rs34520435	0.85[EUR][1000 genomes]
rs34612783	0.83[EUR][1000 genomes]
rs34614087	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34640766	0.85[EUR][1000 genomes]
rs34866877	0.92[EUR][1000 genomes]
rs34896026	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34966024	1.00[ASN][1000 genomes]
rs35073881	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35080938	0.96[EUR][1000 genomes]
rs35081015	0.91[EUR][1000 genomes]
rs35225175	0.91[EUR][1000 genomes]
rs35242294	0.97[EUR][1000 genomes]
rs35251663	0.84[EUR][1000 genomes]
rs35407078	0.92[EUR][1000 genomes]
rs35439100	0.92[EUR][1000 genomes]
rs35440408	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35440822	0.85[EUR][1000 genomes]
rs35461301	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35566812	0.82[EUR][1000 genomes]
rs35609883	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642890	0.85[EUR][1000 genomes]
rs35696739	0.85[EUR][1000 genomes]
rs35828379	0.94[EUR][1000 genomes]
rs35851452	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35873865	0.82[EUR][1000 genomes]
rs35886823	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022925	0.85[EUR][1000 genomes]
rs36037734	0.85[EUR][1000 genomes]
rs36094082	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4299824	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4348308	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4371846	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4415160	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]
rs4457154	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4532444	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4587171	0.81[ASW][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs56037312	0.82[EUR][1000 genomes]
rs58980183	1.00[ASN][1000 genomes]
rs59432342	0.85[EUR][1000 genomes]
rs60163288	1.00[ASN][1000 genomes]
rs61601344	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411372	0.83[EUR][1000 genomes]
rs62411375	0.84[EUR][1000 genomes]
rs62411376	0.85[EUR][1000 genomes]
rs6904535	1.00[ASN][1000 genomes]
rs6905603	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6905658	0.87[ASN][1000 genomes]
rs6910414	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914293	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6918949	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6925518	0.87[ASN][1000 genomes]
rs6926742	0.87[ASN][1000 genomes]
rs6934714	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564854	0.85[EUR][1000 genomes]
rs71564855	0.85[EUR][1000 genomes]
rs71564856	0.85[EUR][1000 genomes]
rs71564861	0.85[EUR][1000 genomes]
rs71564863	0.95[EUR][1000 genomes]
rs7744240	0.81[TSI][hapmap]
rs7749100	1.00[CHD][hapmap]
rs7758867	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap]
rs7761501	0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7761729	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7766565	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7771085	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs7775182	0.84[AMR][1000 genomes];0.92[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1903332	BMP5	cis	cerebellum	SCAN
rs1903332	RAB23	cis	multi-tissue	Pritchard
rs1903332	BEND6	cis	parietal	SCAN
rs1903332	DST	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56716800-56724600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:56716800-56727200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:56717000-56727200	Weak transcription	Psoas Muscle	Psoas
4	chr6:56717400-56724600	Weak transcription	HSMM	muscle
5	chr6:56717400-56730200	Weak transcription	Ovary	ovary
6	chr6:56717800-56724600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:56717800-56724800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:56717800-56724800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:56717800-56724800	Weak transcription	NHLF	lung
10	chr6:56717800-56725000	Weak transcription	HUVEC	blood vessel
11	chr6:56717800-56725000	Weak transcription	NH-A	brain
12	chr6:56717800-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:56717800-56727000	Weak transcription	GM12878-XiMat	blood
14	chr6:56717800-56727400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:56717800-56730400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:56718000-56724600	Weak transcription	A549	lung
17	chr6:56718200-56731000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:56718400-56724800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:56718800-56725200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:56719200-56724600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:56719800-56725000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:56720000-56724800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:56721200-56724600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:56721200-56727400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:56721200-56727800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:56721600-56724600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:56721800-56724800	Weak transcription	Osteobl	bone
28	chr6:56721800-56731200	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:56722000-56724800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:56722000-56724800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:56722000-56724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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