Variant report

Variant	rs1801394
Chromosome Location	chr5:7870973-7870974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:7868367-7870981	K562	blood:	n/a	n/a
2	HCFC1	chr5:7868144-7871042	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr5:7870933-7870979	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7849253..7853514-chr5:7868734..7871211,5	MCF-7	breast:

Variant related genes	Relation type
MTRR	TF binding region
FASTKD3	TF binding region
ENSG00000215217	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11134265	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12653464	1.00[ASN][1000 genomes]
rs2307116	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3733784	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4277880	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1801394	MTRR	cis	multi-tissue	Pritchard
rs1801394	MTRR	cis	Temporal Cortex	GTEx
rs1801394	MTRR	cis	Cerebellum	GTEx
rs1801394	MTRR	cis	Frontal Cortex	GTEx
rs1801394	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7868200-7871000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr5:7869800-7871000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr5:7869800-7871000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:7869800-7871200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:7870000-7871000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:7870000-7871000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr5:7870000-7871000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:7870000-7871000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr5:7870000-7873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:7870000-7875400	Weak transcription	Spleen	Spleen
11	chr5:7870200-7871000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:7870200-7871000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:7870200-7871000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:7870200-7871000	Enhancers	Thymus	Thymus
15	chr5:7870200-7871200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:7870200-7871200	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr5:7870200-7871400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:7870200-7871400	Weak transcription	Left Ventricle	heart
19	chr5:7870200-7871400	Flanking Active TSS	Hela-S3	cervix
20	chr5:7870200-7871600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:7870200-7871600	Weak transcription	Placenta	Placenta
22	chr5:7870200-7871600	Weak transcription	Lung	lung
23	chr5:7870200-7871800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:7870200-7872000	Enhancers	Primary B cells from peripheral blood	blood
25	chr5:7870200-7872000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr5:7870200-7873400	Flanking Active TSS	GM12878-XiMat	blood
27	chr5:7870200-7875400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:7870200-7875600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:7870200-7875600	Weak transcription	HSMMtube	muscle
30	chr5:7870200-7875800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:7870200-7875800	Weak transcription	Esophagus	oesophagus
32	chr5:7870200-7875800	Weak transcription	Gastric	stomach
33	chr5:7870200-7876000	Weak transcription	Fetal Brain Male	brain
34	chr5:7870200-7879800	Weak transcription	Pancreas	Pancrea
35	chr5:7870200-7882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:7870400-7871000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:7870400-7871000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr5:7870400-7871000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr5:7870400-7871000	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr5:7870400-7871000	Enhancers	Colon Smooth Muscle	Colon
42	chr5:7870400-7871000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr5:7870400-7871000	Enhancers	Fetal Heart	heart
44	chr5:7870400-7871000	Weak transcription	Fetal Intestine Large	intestine
45	chr5:7870400-7871000	Enhancers	Ovary	ovary
46	chr5:7870400-7871000	Flanking Active TSS	NHDF-Ad	bronchial
47	chr5:7870400-7871200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:7870400-7871200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr5:7870400-7871200	Flanking Active TSS	A549	lung
50	chr5:7870400-7871400	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links