Variant report

Variant	rs25908
Chromosome Location	chr5:16776951-16776952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16740780..16741704-chr5:16776541..16777578,3	MCF-7	breast:
2	chr5:16690107..16691016-chr5:16776506..16777632,8	MCF-7	breast:
3	chr5:16690101..16691036-chr5:16776467..16777868,10	MCF-7	breast:
4	chr5:16679668..16680619-chr5:16776494..16777357,4	MCF-7	breast:
5	chr5:16740840..16741721-chr5:16776516..16777353,6	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs250344	1.00[CEU][hapmap]
rs2561232	0.85[AMR][1000 genomes]
rs2561233	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs25904	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs25905	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs25907	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs31511	0.85[AMR][1000 genomes]
rs31571	1.00[CEU][hapmap];0.96[AMR][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	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16736400-16781400	Weak transcription	Esophagus	oesophagus
2	chr5:16737000-16780400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:16741200-16782000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:16743600-16777600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:16746000-16778200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:16748600-16783800	Weak transcription	Small Intestine	intestine
7	chr5:16755200-16795400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:16757600-16796800	Weak transcription	Right Ventricle	heart
9	chr5:16758400-16779200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:16759800-16783600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:16760000-16791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:16761000-16796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:16762400-16784000	Weak transcription	Colonic Mucosa	Colon
14	chr5:16763200-16782200	Weak transcription	Fetal Brain Male	brain
15	chr5:16763800-16794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:16764200-16784000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:16764600-16777400	Weak transcription	Aorta	Aorta
18	chr5:16764600-16783800	Weak transcription	Spleen	Spleen
19	chr5:16764600-16792800	Weak transcription	Stomach Mucosa	stomach
20	chr5:16764600-16807400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:16766800-16785200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:16767200-16781800	Weak transcription	Ovary	ovary
23	chr5:16768600-16781800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:16769200-16781800	Weak transcription	Lung	lung
25	chr5:16769400-16778200	Weak transcription	Gastric	stomach
26	chr5:16770000-16777600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:16770200-16777600	Weak transcription	HSMMtube	muscle
28	chr5:16770200-16778200	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:16770200-16791400	Weak transcription	Fetal Kidney	kidney
30	chr5:16770400-16778200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:16770800-16778400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:16770800-16778400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:16770800-16792400	Weak transcription	Placenta	Placenta
34	chr5:16770800-16793800	Weak transcription	Hela-S3	cervix
35	chr5:16771000-16777200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:16771000-16777600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:16771000-16779200	Weak transcription	Pancreas	Pancrea
38	chr5:16771000-16781600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:16771200-16778200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:16771400-16777200	Weak transcription	Fetal Intestine Small	intestine
41	chr5:16771400-16778200	Weak transcription	Fetal Intestine Large	intestine
42	chr5:16771400-16778400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:16773200-16781800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:16773600-16777600	Weak transcription	Fetal Lung	lung
45	chr5:16774000-16777400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:16774200-16777000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:16774200-16779000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:16774400-16777200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:16774400-16777600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:16774400-16778800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links