Variant report

Variant	rs162029
Chromosome Location	chr5:7865527-7865528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:7856634..7862841-chr5:7863423..7866521,7	MCF-7	breast:
2	chr5:7861150..7864391-chr5:7864437..7866400,3	K562	blood:
3	chr5:7857476..7859602-chr5:7864063..7866187,3	K562	blood:
4	chr5:7860007..7862983-chr5:7864596..7866833,2	K562	blood:

Variant related genes	Relation type
ENSG00000124279	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11134265	0.82[YRI][hapmap]
rs161871	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs162024	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs162047	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs162050	0.83[EUR][1000 genomes]
rs3733784	0.83[ASW][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs162029	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs162029	FASTKD3	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
2	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:7852200-7868400	Weak transcription	Gastric	stomach
7	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:7852400-7867800	Weak transcription	Fetal Brain Male	brain
9	chr5:7852800-7868400	Weak transcription	Pancreas	Pancrea
10	chr5:7854000-7868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:7856000-7868400	Weak transcription	Stomach Mucosa	stomach
12	chr5:7856600-7867600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:7857600-7867800	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:7857800-7865800	Strong transcription	Fetal Intestine Large	intestine
15	chr5:7857800-7866000	Strong transcription	Liver	Liver
16	chr5:7857800-7866200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr5:7857800-7866200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr5:7857800-7866600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:7858000-7866000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:7858000-7866600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:7858000-7867200	Strong transcription	HSMM	muscle
22	chr5:7858000-7867400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:7858200-7866600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:7858200-7867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:7858400-7865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:7858400-7866200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:7858400-7868200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:7858600-7865600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:7858600-7866000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:7858800-7865800	Strong transcription	Hela-S3	cervix
31	chr5:7858800-7865800	Strong transcription	K562	blood
32	chr5:7858800-7868400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:7859000-7866000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:7859000-7866200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:7859400-7866400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:7859600-7866000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:7859600-7866200	Strong transcription	A549	lung
38	chr5:7859600-7866600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:7859600-7866800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:7859600-7867400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:7860400-7866600	Weak transcription	Spleen	Spleen
42	chr5:7860400-7868000	Weak transcription	Esophagus	oesophagus
43	chr5:7860400-7868400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:7861000-7865600	Strong transcription	HepG2	liver
45	chr5:7861000-7866600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:7861400-7866200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:7862400-7867400	Weak transcription	Left Ventricle	heart
48	chr5:7862400-7867600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:7862400-7868000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:7862400-7868000	Weak transcription	Lung	lung

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