Variant report

Variant	rs4587171
Chromosome Location	chr6:56670263-56670264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56669458..56671169-chr6:56819169..56820838,2	MCF-7	breast:
2	chr6:56669642..56671270-chr6:56707405..56709365,2	MCF-7	breast:
3	chr6:56667404..56671001-chr6:56671318..56674766,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231441	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10498812	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs10498813	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs11756551	0.90[EUR][1000 genomes]
rs11970648	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs13190854	0.89[EUR][1000 genomes]
rs13192540	0.86[EUR][1000 genomes]
rs13192931	0.86[EUR][1000 genomes]
rs13194625	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs13194904	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs13195601	0.89[EUR][1000 genomes]
rs13198204	0.97[EUR][1000 genomes]
rs13198597	0.83[EUR][1000 genomes]
rs13200166	0.83[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs13200559	0.89[EUR][1000 genomes]
rs13200768	0.92[EUR][1000 genomes]
rs13200868	0.86[EUR][1000 genomes]
rs13201639	0.97[EUR][1000 genomes]
rs13201733	0.97[EUR][1000 genomes]
rs13203148	0.90[EUR][1000 genomes]
rs13203327	0.90[EUR][1000 genomes]
rs13203681	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs13204466	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs13205667	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs13207768	0.83[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13208409	0.86[EUR][1000 genomes]
rs13211879	0.87[EUR][1000 genomes]
rs13214893	0.81[EUR][1000 genomes]
rs13215883	0.83[EUR][1000 genomes]
rs13218913	0.83[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs13220618	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs13220628	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs13220851	0.95[EUR][1000 genomes]
rs1610157	0.85[EUR][1000 genomes]
rs16888171	0.83[CEU][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs16888184	0.82[EUR][1000 genomes]
rs16888186	0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs16888189	0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap]
rs16888192	0.92[CHB][hapmap]
rs17684730	0.97[EUR][1000 genomes]
rs17684748	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs17684772	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs17684784	0.83[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs17684802	0.83[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs17684878	0.83[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs17684884	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs17684941	0.82[EUR][1000 genomes]
rs17751966	0.82[CEU][hapmap];0.97[EUR][1000 genomes]
rs17751977	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs17752002	0.95[EUR][1000 genomes]
rs17752046	0.83[CEU][hapmap];0.95[EUR][1000 genomes]
rs17752106	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs17752213	0.81[EUR][1000 genomes]
rs17831310	0.84[ASN][1000 genomes]
rs1903332	0.81[ASW][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs28360570	0.83[EUR][1000 genomes]
rs34083827	0.80[EUR][1000 genomes]
rs34171958	0.96[EUR][1000 genomes]
rs34228698	0.94[EUR][1000 genomes]
rs34359353	0.96[EUR][1000 genomes]
rs34425815	0.95[EUR][1000 genomes]
rs34500949	0.87[EUR][1000 genomes]
rs34520435	0.96[EUR][1000 genomes]
rs34612783	0.92[EUR][1000 genomes]
rs34614087	0.89[EUR][1000 genomes]
rs34640766	0.95[EUR][1000 genomes]
rs34866877	0.89[EUR][1000 genomes]
rs34896026	0.89[EUR][1000 genomes]
rs34966024	0.87[EUR][1000 genomes]
rs35073881	0.86[EUR][1000 genomes]
rs35080938	0.86[EUR][1000 genomes]
rs35081015	0.90[EUR][1000 genomes]
rs35225175	0.90[EUR][1000 genomes]
rs35242294	0.85[EUR][1000 genomes]
rs35251663	0.96[EUR][1000 genomes]
rs35407078	0.89[EUR][1000 genomes]
rs35439100	0.89[EUR][1000 genomes]
rs35440408	0.80[EUR][1000 genomes]
rs35440822	0.96[EUR][1000 genomes]
rs35461301	0.89[EUR][1000 genomes]
rs35566812	0.92[EUR][1000 genomes]
rs35609883	0.97[EUR][1000 genomes]
rs35642890	0.97[EUR][1000 genomes]
rs35696739	0.97[EUR][1000 genomes]
rs35828379	0.86[EUR][1000 genomes]
rs35851452	0.89[EUR][1000 genomes]
rs35873865	0.92[EUR][1000 genomes]
rs35886823	0.95[EUR][1000 genomes]
rs35986172	0.86[EUR][1000 genomes]
rs36022925	0.95[EUR][1000 genomes]
rs36037734	0.97[EUR][1000 genomes]
rs36094082	0.86[EUR][1000 genomes]
rs4299824	0.83[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4348308	0.83[CEU][hapmap];0.95[EUR][1000 genomes]
rs4371846	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs4415160	0.83[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4457154	0.83[CEU][hapmap];0.97[EUR][1000 genomes]
rs4532444	0.89[EUR][1000 genomes]
rs4568454	0.84[ASN][1000 genomes]
rs56368885	0.87[EUR][1000 genomes]
rs58980183	0.87[EUR][1000 genomes]
rs59432342	0.94[EUR][1000 genomes]
rs61601344	0.94[EUR][1000 genomes]
rs62411366	0.86[EUR][1000 genomes]
rs62411367	0.89[EUR][1000 genomes]
rs62411372	0.92[EUR][1000 genomes]
rs62411375	0.93[EUR][1000 genomes]
rs62411376	0.94[EUR][1000 genomes]
rs6904535	0.89[EUR][1000 genomes]
rs6905603	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6910414	0.81[EUR][1000 genomes]
rs6914293	0.85[EUR][1000 genomes]
rs6918949	0.83[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6928104	0.86[EUR][1000 genomes]
rs6934714	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs71564854	0.94[EUR][1000 genomes]
rs71564855	0.96[EUR][1000 genomes]
rs71564856	0.97[EUR][1000 genomes]
rs71564861	0.97[EUR][1000 genomes]
rs71564863	0.86[EUR][1000 genomes]
rs7744240	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs7758867	0.94[ASW][hapmap];0.83[CEU][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7761501	0.83[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7761729	0.83[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7766565	0.80[EUR][1000 genomes]
rs7771085	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs7775182	0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4587171	BMP5	cis	cerebellum	SCAN
rs4587171	DST	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56659400-56674000	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56659800-56671000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56661400-56672800	Weak transcription	Ovary	ovary
4	chr6:56662600-56672800	Weak transcription	Left Ventricle	heart
5	chr6:56663000-56671200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56664000-56673600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:56664200-56671200	Weak transcription	Psoas Muscle	Psoas
8	chr6:56667000-56671800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:56667200-56670800	Enhancers	HUVEC	blood vessel
10	chr6:56667200-56671200	Enhancers	Brain Angular Gyrus	brain
11	chr6:56667200-56671200	Enhancers	Osteobl	bone
12	chr6:56667200-56671600	Enhancers	NHLF	lung
13	chr6:56667200-56672800	Enhancers	Brain Substantia Nigra	brain
14	chr6:56667200-56673600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:56667200-56674600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:56667400-56671000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:56667400-56671600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr6:56667400-56671800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:56667400-56672000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56667400-56673600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:56667400-56673600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:56667400-56674200	Enhancers	Brain Anterior Caudate	brain
23	chr6:56667400-56674200	Enhancers	Brain Hippocampus Middle	brain
24	chr6:56667400-56674600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr6:56667600-56671400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:56667600-56671600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:56667600-56672800	Weak transcription	Right Atrium	heart
28	chr6:56668000-56672400	Weak transcription	HMEC	breast
29	chr6:56668000-56674400	Enhancers	NH-A	brain
30	chr6:56668000-56679200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:56668200-56671400	Enhancers	HSMM	muscle
32	chr6:56668400-56670800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:56668600-56671800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:56668800-56670400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:56668800-56671200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:56668800-56672200	Weak transcription	Hela-S3	cervix
37	chr6:56668800-56672800	Weak transcription	Right Ventricle	heart
38	chr6:56668800-56673000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:56668800-56682600	Weak transcription	Aorta	Aorta
40	chr6:56669000-56670600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:56669000-56670600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:56669000-56670600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:56669000-56671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:56669000-56673400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:56669200-56670400	Enhancers	NHEK	skin
46	chr6:56669200-56670800	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr6:56669200-56671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:56669400-56670600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:56669400-56671600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:56669400-56672000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links