Variant report

Variant	rs6461887
Chromosome Location	chr7:25885411-25885412
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	chr7:25883299..25886536-chr7:25889518..25893858,4	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10225976	0.96[EUR][1000 genomes]
rs10232819	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241659	0.96[EUR][1000 genomes]
rs10261019	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10271088	0.95[EUR][1000 genomes]
rs10271460	0.96[EUR][1000 genomes]
rs10274306	0.96[EUR][1000 genomes]
rs10951112	0.93[ASN][1000 genomes]
rs11976790	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535837	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12700664	0.81[ASN][1000 genomes]
rs12700666	0.81[ASN][1000 genomes]
rs12700667	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13231733	0.81[ASN][1000 genomes]
rs1376527	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451382	0.96[EUR][1000 genomes]
rs1451383	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1451385	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060765	0.86[EUR][1000 genomes]
rs2893220	0.96[EUR][1000 genomes]
rs3902751	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722526	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722527	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722528	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4722529	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722530	0.93[ASN][1000 genomes]
rs4722531	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376645	0.97[EUR][1000 genomes]
rs60643312	0.96[EUR][1000 genomes]
rs61140461	0.96[EUR][1000 genomes]
rs62447896	0.96[EUR][1000 genomes]
rs6958350	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961848	0.81[ASN][1000 genomes]
rs7782246	0.95[EUR][1000 genomes]
rs7782292	0.96[EUR][1000 genomes]
rs7793216	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798431	0.96[EUR][1000 genomes]
rs979165	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987000	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830928	chr7:25820147-25965014	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25872200-25886200	Weak transcription	NHLF	lung
2	chr7:25880000-25888800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:25880000-25889000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr7:25881800-25889000	Enhancers	Osteobl	bone
5	chr7:25882200-25885600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr7:25882200-25892000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:25882600-25885600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:25882800-25886600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:25883000-25887000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:25883200-25887200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:25883400-25886400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:25883400-25889000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:25883400-25891000	Enhancers	Stomach Smooth Muscle	stomach
14	chr7:25883400-25891200	Enhancers	Fetal Heart	heart
15	chr7:25883800-25885800	Enhancers	Aorta	Aorta
16	chr7:25883800-25892600	Enhancers	Fetal Lung	lung
17	chr7:25884000-25885600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:25884000-25886600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:25884400-25885800	Enhancers	Fetal Intestine Small	intestine
20	chr7:25884400-25887000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:25884600-25885600	Enhancers	Fetal Intestine Large	intestine
22	chr7:25884600-25885600	Weak transcription	HSMMtube	muscle
23	chr7:25884600-25886400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:25884600-25889000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr7:25884600-25890600	Enhancers	Fetal Stomach	stomach
26	chr7:25884600-25890800	Enhancers	Placenta	Placenta
27	chr7:25884800-25885600	Enhancers	Left Ventricle	heart
28	chr7:25884800-25886000	Weak transcription	HSMM	muscle
29	chr7:25884800-25886200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:25884800-25889800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr7:25885000-25886200	Weak transcription	NHDF-Ad	bronchial
32	chr7:25885000-25888200	Enhancers	Fetal Kidney	kidney
33	chr7:25885200-25885600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:25885200-25885800	Enhancers	Right Atrium	heart
35	chr7:25885200-25885800	Enhancers	Right Ventricle	heart
36	chr7:25885200-25886000	Enhancers	Pancreas	Pancrea
37	chr7:25885200-25887000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr7:25885200-25887800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr7:25885200-25887800	Enhancers	Ovary	ovary
40	chr7:25885200-25889000	Enhancers	Adipose Nuclei	Adipose
41	chr7:25885200-25890800	Enhancers	Fetal Muscle Leg	muscle
42	chr7:25885400-25885800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:25885400-25885800	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr7:25885400-25885800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr7:25885400-25885800	Weak transcription	NH-A	brain
46	chr7:25885400-25887400	Enhancers	Psoas Muscle	Psoas
47	chr7:25885400-25887600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:25885400-25887600	Enhancers	Brain Anterior Caudate	brain
49	chr7:25885400-25889000	Weak transcription	K562	blood
50	chr7:25885400-25890800	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links