Variant report

Variant	rs6904535
Chromosome Location	chr6:56631976-56631977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56630082..56632054-chr6:56636880..56638995,2	K562	blood:

Extended variants
information (count: 165 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap]
rs10498812	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11756551	0.98[EUR][1000 genomes]
rs11961141	0.82[AMR][1000 genomes]
rs11961342	0.82[AMR][1000 genomes]
rs11968575	0.81[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs11970648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13190784	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs13190854	0.87[EUR][1000 genomes]
rs13191826	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13192478	0.82[AMR][1000 genomes]
rs13192540	0.84[EUR][1000 genomes]
rs13192567	0.82[AMR][1000 genomes]
rs13192931	0.84[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13195601	0.87[EUR][1000 genomes]
rs13198204	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13198399	0.83[AMR][1000 genomes]
rs13198597	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs13200166	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13200559	1.00[EUR][1000 genomes]
rs13200768	0.96[EUR][1000 genomes]
rs13200868	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201639	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13201733	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap]
rs13203148	0.88[EUR][1000 genomes]
rs13203327	0.94[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs13208409	0.97[EUR][1000 genomes]
rs13210876	0.83[AMR][1000 genomes]
rs13211879	0.86[EUR][1000 genomes]
rs13213878	0.81[AMR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap]
rs13218913	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13219546	0.83[AMR][1000 genomes]
rs13220618	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13220851	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1610157	0.82[EUR][1000 genomes]
rs16888135	0.83[AMR][1000 genomes]
rs16888171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17684730	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684802	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684878	1.00[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17751682	0.90[MEX][hapmap]
rs17751695	0.90[MEX][hapmap]
rs17751966	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17752002	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs28360570	0.80[EUR][1000 genomes]
rs2967960	0.83[AMR][1000 genomes]
rs2967963	0.81[AMR][1000 genomes]
rs3002003	0.83[AMR][1000 genomes]
rs3002004	0.83[AMR][1000 genomes]
rs3002006	0.83[AMR][1000 genomes]
rs3002007	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3002008	0.83[AMR][1000 genomes]
rs3002009	0.80[AMR][1000 genomes]
rs3002010	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs3002011	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs34171958	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34228698	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34359353	0.91[EUR][1000 genomes]
rs34425815	0.89[EUR][1000 genomes]
rs34500949	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34520435	0.91[EUR][1000 genomes]
rs34612783	0.96[EUR][1000 genomes]
rs34614087	0.87[EUR][1000 genomes]
rs34640766	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34812826	0.82[AMR][1000 genomes]
rs34824960	0.82[AMR][1000 genomes]
rs34866877	0.87[EUR][1000 genomes]
rs34896026	0.87[EUR][1000 genomes]
rs34966024	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35073881	0.84[EUR][1000 genomes]
rs35080938	0.83[EUR][1000 genomes]
rs35081015	0.88[EUR][1000 genomes]
rs35225175	0.88[EUR][1000 genomes]
rs35242294	0.82[EUR][1000 genomes]
rs35251663	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35407078	0.87[EUR][1000 genomes]
rs35439100	0.87[EUR][1000 genomes]
rs35440408	1.00[ASN][1000 genomes]
rs35440822	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35461301	0.87[EUR][1000 genomes]
rs35566812	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35609883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642890	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35696739	0.92[EUR][1000 genomes]
rs35828379	0.83[EUR][1000 genomes]
rs35851452	0.87[EUR][1000 genomes]
rs35873865	0.95[EUR][1000 genomes]
rs35886823	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35920751	0.82[AMR][1000 genomes]
rs35986172	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36022925	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36037734	0.92[EUR][1000 genomes]
rs36068365	0.82[AMR][1000 genomes]
rs36094082	0.84[EUR][1000 genomes]
rs4074101	0.90[MEX][hapmap]
rs4275049	0.83[AMR][1000 genomes]
rs4299824	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4415160	1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4532444	0.88[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4640889	0.83[AMR][1000 genomes]
rs56368885	0.98[EUR][1000 genomes]
rs58980183	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59085778	0.82[AMR][1000 genomes]
rs59247267	0.83[AMR][1000 genomes]
rs59432342	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60163288	1.00[ASN][1000 genomes]
rs61601344	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411366	0.98[EUR][1000 genomes]
rs62411367	1.00[EUR][1000 genomes]
rs62411372	0.96[EUR][1000 genomes]
rs62411375	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62411376	0.95[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6905658	0.87[ASN][1000 genomes]
rs6910414	1.00[ASN][1000 genomes]
rs6914293	0.82[EUR][1000 genomes]
rs6918949	1.00[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6925518	0.87[ASN][1000 genomes]
rs6926134	0.83[AMR][1000 genomes]
rs6926742	0.87[ASN][1000 genomes]
rs6928104	0.98[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938003	0.81[AMR][1000 genomes]
rs71564854	0.95[EUR][1000 genomes]
rs71564855	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71564856	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564861	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564863	0.84[EUR][1000 genomes]
rs7749100	1.00[CHD][hapmap]
rs7758867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap]
rs7761501	1.00[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7775134	1.00[CHD][hapmap]
rs7775182	0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6904535	BMP5	cis	cerebellum	SCAN
rs6904535	DST	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56621400-56634200	Weak transcription	Spleen	Spleen
2	chr6:56622400-56637600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:56623600-56637200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:56623600-56637600	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:56625200-56637800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:56625600-56637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain
8	chr6:56625800-56637000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:56626400-56637200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:56626600-56636000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:56627200-56637400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:56627800-56633000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:56627800-56633400	Enhancers	Colon Smooth Muscle	Colon
14	chr6:56628200-56638400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:56628400-56633000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:56628400-56638400	Enhancers	Osteobl	bone
17	chr6:56628600-56632000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr6:56628600-56632000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:56628600-56632000	Enhancers	Fetal Heart	heart
20	chr6:56628600-56633200	Enhancers	Brain Hippocampus Middle	brain
21	chr6:56628600-56634400	Enhancers	Brain Cingulate Gyrus	brain
22	chr6:56628600-56638200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:56628600-56638400	Enhancers	HSMM	muscle
24	chr6:56628800-56632800	Enhancers	NHDF-Ad	bronchial
25	chr6:56629200-56637600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:56629400-56632600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:56629400-56634200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:56629400-56634200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:56629400-56637000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:56629400-56637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:56629400-56637600	Weak transcription	Aorta	Aorta
32	chr6:56629400-56640400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:56629600-56632600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:56629600-56637600	Weak transcription	Ovary	ovary
35	chr6:56629800-56633000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:56630000-56632800	Enhancers	NHLF	lung
37	chr6:56630000-56633600	Enhancers	Brain Anterior Caudate	brain
38	chr6:56630000-56634600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:56630000-56638000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:56630000-56638200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:56630000-56638400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:56630200-56632800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:56630200-56638200	Enhancers	HSMMtube	muscle
44	chr6:56630400-56635600	Weak transcription	HUVEC	blood vessel
45	chr6:56630600-56633200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:56630800-56633200	Enhancers	NH-A	brain
47	chr6:56631000-56632000	Enhancers	Fetal Lung	lung
48	chr6:56631000-56632000	Enhancers	A549	lung
49	chr6:56631000-56632200	Enhancers	Hela-S3	cervix
50	chr6:56631000-56632800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links