Variant report

Variant	rs4425464
Chromosome Location	chr5:68720856-68720857
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	chr5:68720210..68723027-chr5:68724796..68726675,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1006633	0.93[ASN][1000 genomes]
rs10940223	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11948450	0.90[ASN][1000 genomes]
rs11948887	0.93[ASN][1000 genomes]
rs11952246	0.93[ASN][1000 genomes]
rs12516805	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12654780	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12655061	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657358	0.96[ASN][1000 genomes]
rs12658657	0.96[ASN][1000 genomes]
rs12659035	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1441800	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236632	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010354	0.93[ASN][1000 genomes]
rs28670985	0.82[ASN][1000 genomes]
rs28687907	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28817404	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756399	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756400	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756402	0.96[ASN][1000 genomes]
rs4252221	0.96[ASN][1000 genomes]
rs4976195	0.90[ASN][1000 genomes]
rs4976197	0.96[ASN][1000 genomes]
rs6450039	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6450041	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6870267	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871685	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72647235	0.90[ASN][1000 genomes]
rs72647237	0.93[ASN][1000 genomes]
rs7729938	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68711600-68722800	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:68711600-68724000	Weak transcription	Right Atrium	heart
3	chr5:68711800-68723600	Weak transcription	Small Intestine	intestine
4	chr5:68711800-68725000	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:68711800-68731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:68712400-68731000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:68712400-68735600	Weak transcription	Hela-S3	cervix
8	chr5:68712400-68739000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:68712400-68740400	Weak transcription	Fetal Kidney	kidney
10	chr5:68712800-68738200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:68714400-68723800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:68716000-68728800	Weak transcription	Lung	lung
13	chr5:68716000-68732200	Weak transcription	Esophagus	oesophagus
14	chr5:68716000-68733600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:68716000-68735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:68716000-68738200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:68716000-68738800	Weak transcription	Fetal Stomach	stomach
18	chr5:68716200-68724800	Weak transcription	Stomach Mucosa	stomach
19	chr5:68716200-68728200	Weak transcription	Liver	Liver
20	chr5:68716200-68728400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:68716200-68728400	Weak transcription	Placenta	Placenta
22	chr5:68716200-68738000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:68716400-68728200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:68716400-68728400	Weak transcription	HMEC	breast
25	chr5:68716400-68729000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:68716400-68729800	Weak transcription	NHEK	skin
27	chr5:68716400-68742000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:68716600-68728400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:68716600-68729800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:68716800-68727400	Weak transcription	HepG2	liver
31	chr5:68716800-68728400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:68717400-68728200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:68719000-68728400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:68719200-68722800	Weak transcription	Fetal Intestine Large	intestine
35	chr5:68719200-68724600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:68719200-68727400	Weak transcription	Pancreas	Pancrea
37	chr5:68719200-68728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:68719200-68728400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:68719200-68733000	Strong transcription	Fetal Intestine Small	intestine
40	chr5:68719400-68729800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:68719400-68731800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:68719400-68733600	Weak transcription	Gastric	stomach
43	chr5:68720400-68727400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:68720800-68724400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:68720800-68724600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:68720800-68728200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:68720800-68728400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links