Variant report

Variant	rs6725704
Chromosome Location	chr2:39685092-39685093
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	chr2:39680725..39683099-chr2:39684790..39686742,2	MCF-7	breast:
2	chr2:39684833..39686565-chr2:39689328..39692216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12105018	0.84[AMR][1000 genomes]
rs17023486	0.93[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs57107827	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57164521	0.92[AMR][1000 genomes]
rs58019817	0.92[AMR][1000 genomes]
rs61344670	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6706951	0.92[AMR][1000 genomes]
rs6722096	0.92[AMR][1000 genomes]
rs6725496	0.92[AMR][1000 genomes]
rs6725849	0.87[LWK][hapmap];1.00[MEX][hapmap]
rs6759388	0.84[AMR][1000 genomes]
rs72914206	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72925278	0.92[AMR][1000 genomes]
rs72925283	0.92[AMR][1000 genomes]
rs72925290	0.92[AMR][1000 genomes]
rs72927103	0.92[AMR][1000 genomes]
rs72927107	0.92[AMR][1000 genomes]
rs72927108	0.92[AMR][1000 genomes]
rs72927110	0.92[AMR][1000 genomes]
rs72927119	0.92[AMR][1000 genomes]
rs72927143	0.92[AMR][1000 genomes]
rs72929164	0.84[AMR][1000 genomes]
rs72929184	0.84[AMR][1000 genomes]
rs72931129	0.84[AMR][1000 genomes]
rs72931131	0.84[AMR][1000 genomes]
rs72931135	0.84[AMR][1000 genomes]
rs72931145	0.84[AMR][1000 genomes]
rs72931150	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72931159	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72931161	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72931172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7566368	0.84[AMR][1000 genomes]
rs7581123	0.84[AMR][1000 genomes]
rs7592925	0.87[ASW][hapmap];0.92[LWK][hapmap];0.84[AMR][1000 genomes]
rs7609233	0.81[AFR][1000 genomes];0.84[AMR][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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39685600	Weak transcription	Left Ventricle	heart
3	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
5	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
7	chr2:39667200-39685200	Weak transcription	NHEK	skin
8	chr2:39667200-39694600	Weak transcription	NHLF	lung
9	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
10	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
11	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
15	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
16	chr2:39675200-39686000	Weak transcription	NHDF-Ad	bronchial
17	chr2:39675400-39694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:39677200-39687400	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:39678000-39696800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:39678200-39694600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:39681000-39686200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:39682200-39692000	Weak transcription	Fetal Lung	lung
23	chr2:39682200-39695600	Weak transcription	Fetal Brain Male	brain
24	chr2:39682400-39686000	Weak transcription	Liver	Liver
25	chr2:39682400-39694600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:39682600-39685800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:39682600-39687200	Weak transcription	Adipose Nuclei	Adipose
28	chr2:39682600-39694800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:39682600-39695600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:39682600-39695800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:39682800-39694400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:39682800-39694600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:39683000-39694600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:39683200-39685800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:39683200-39686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:39683200-39694400	Weak transcription	HepG2	liver
37	chr2:39683200-39694600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:39683200-39694600	Weak transcription	Ovary	ovary
39	chr2:39683200-39694800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:39683400-39694800	Weak transcription	NH-A	brain
41	chr2:39684400-39686400	Strong transcription	HSMM	muscle
42	chr2:39684600-39686000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:39684600-39687600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:39684800-39685200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr2:39684800-39685200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr2:39684800-39685200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:39684800-39685200	ZNF genes & repeats	Fetal Intestine Large	intestine
48	chr2:39684800-39685200	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr2:39684800-39685200	ZNF genes & repeats	Placenta	Placenta
50	chr2:39684800-39685400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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