Variant report

Variant	rs3002007
Chromosome Location	chr6:56618760-56618761
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56614450..56616010-chr6:56617525..56619069,2	MCF-7	breast:

Extended variants
information (count: 143 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap]
rs10498811	0.81[EUR][1000 genomes]
rs10498812	0.81[CEU][hapmap]
rs10498813	0.81[CEU][hapmap]
rs11961141	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11968575	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970648	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190784	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191164	0.81[EUR][1000 genomes]
rs13192037	0.81[EUR][1000 genomes]
rs13192478	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194625	0.81[CEU][hapmap]
rs13194904	0.81[CEU][hapmap]
rs13196211	0.81[EUR][1000 genomes]
rs13198399	0.97[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13200166	0.81[CEU][hapmap]
rs13200559	0.80[EUR][1000 genomes]
rs13203000	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13203681	0.81[CEU][hapmap]
rs13204466	0.81[CEU][hapmap]
rs13205013	0.81[EUR][1000 genomes]
rs13205667	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs13206849	0.81[EUR][1000 genomes]
rs13207768	0.81[CEU][hapmap]
rs13208409	0.83[EUR][1000 genomes]
rs13210876	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13218913	0.81[CEU][hapmap]
rs13219546	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.96[EUR][1000 genomes]
rs13220618	0.81[CEU][hapmap]
rs13220628	0.86[CEU][hapmap]
rs16888118	0.81[EUR][1000 genomes]
rs16888124	0.81[EUR][1000 genomes]
rs16888128	0.83[EUR][1000 genomes]
rs16888130	0.83[EUR][1000 genomes]
rs16888133	0.81[EUR][1000 genomes]
rs16888135	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs16888186	1.00[CHB][hapmap]
rs17684511	0.81[EUR][1000 genomes]
rs17684553	0.83[EUR][1000 genomes]
rs17684571	0.83[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];0.81[EUR][1000 genomes]
rs17751695	0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs17751977	0.81[CEU][hapmap]
rs17752046	0.81[CEU][hapmap]
rs17752106	0.81[CEU][hapmap]
rs1903332	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2967960	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002003	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002008	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002009	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34138864	0.81[EUR][1000 genomes]
rs34429594	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34455199	0.98[EUR][1000 genomes]
rs34463732	0.89[EUR][1000 genomes]
rs34465210	0.98[EUR][1000 genomes]
rs34566275	0.98[EUR][1000 genomes]
rs34587484	0.98[EUR][1000 genomes]
rs34623351	0.98[EUR][1000 genomes]
rs34703847	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34724718	0.81[EUR][1000 genomes]
rs34803237	0.98[EUR][1000 genomes]
rs34812826	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.97[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	0.83[EUR][1000 genomes]
rs35326806	0.96[EUR][1000 genomes]
rs35408048	0.81[EUR][1000 genomes]
rs35494794	0.96[EUR][1000 genomes]
rs35619924	0.81[EUR][1000 genomes]
rs35637749	0.81[EUR][1000 genomes]
rs35668437	0.81[EUR][1000 genomes]
rs35687635	0.83[EUR][1000 genomes]
rs35876418	0.98[EUR][1000 genomes]
rs35920751	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4072271	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4074101	0.85[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4074102	0.81[EUR][1000 genomes]
rs41267675	0.98[EUR][1000 genomes]
rs4275049	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024547	0.81[EUR][1000 genomes]
rs55742092	0.81[EUR][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56101897	0.81[EUR][1000 genomes]
rs59085778	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60498201	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62411367	0.80[EUR][1000 genomes]
rs62412526	0.81[EUR][1000 genomes]
rs62412528	0.81[EUR][1000 genomes]
rs62412531	0.81[EUR][1000 genomes]
rs62412532	0.81[EUR][1000 genomes]
rs62412544	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62412556	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6901176	0.81[EUR][1000 genomes]
rs6904535	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6905603	0.81[CEU][hapmap]
rs6918949	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs6924375	0.81[EUR][1000 genomes]
rs6926134	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6934714	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6938003	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564849	0.83[EUR][1000 genomes]
rs7749100	1.00[CHD][hapmap]
rs7758867	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7760542	1.00[CHD][hapmap]
rs7761501	0.81[CEU][hapmap]
rs7761729	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs7767128	0.81[EUR][1000 genomes]
rs7771085	0.80[CEU][hapmap]
rs7775134	1.00[CHD][hapmap]

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
rs3002007	BMP5	cis	cerebellum	SCAN
rs3002007	RAB23	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:56611600-56625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:56612200-56620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:56612400-56621800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:56614000-56621400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:56614200-56619200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:56614200-56619400	Enhancers	Osteobl	bone
11	chr6:56614400-56619400	Enhancers	NHDF-Ad	bronchial
12	chr6:56614400-56619600	Enhancers	Brain Hippocampus Middle	brain
13	chr6:56614800-56620600	Weak transcription	Aorta	Aorta
14	chr6:56615000-56618800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:56615000-56620000	Weak transcription	Psoas Muscle	Psoas
16	chr6:56615000-56620600	Weak transcription	Left Ventricle	heart
17	chr6:56615000-56620800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:56615000-56620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:56615000-56620800	Weak transcription	Right Atrium	heart
20	chr6:56615000-56620800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:56615000-56621000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:56615000-56621400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:56615000-56625000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:56615200-56619600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:56615200-56620800	Weak transcription	Stomach Mucosa	stomach
26	chr6:56615200-56621000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:56615200-56621000	Weak transcription	HUVEC	blood vessel
28	chr6:56615400-56620800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:56615600-56620000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:56615800-56620200	Weak transcription	Fetal Brain Male	brain
31	chr6:56615800-56624000	Enhancers	Fetal Heart	heart
32	chr6:56616600-56620000	Weak transcription	Fetal Lung	lung
33	chr6:56616600-56621000	Weak transcription	HSMMtube	muscle
34	chr6:56616800-56618800	Enhancers	Brain Substantia Nigra	brain
35	chr6:56616800-56620000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:56617000-56618800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:56617000-56620000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:56617000-56620800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:56617200-56618800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:56617200-56624400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:56617200-56624800	Enhancers	Brain Angular Gyrus	brain
42	chr6:56617400-56619800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:56617400-56620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:56617400-56620600	Weak transcription	A549	lung
45	chr6:56617400-56620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:56617400-56621000	Weak transcription	NHEK	skin
47	chr6:56617600-56620200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:56617600-56620800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:56617600-56620800	Weak transcription	NH-A	brain
50	chr6:56617600-56621000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links