Variant report

Variant	rs326120
Chromosome Location	chr5:7874847-7874848
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	ZNF384	chr5:7874585-7875065	K562	blood:	n/a	n/a
2	POLR2A	chr5:7874051-7876125	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:7873979..7876833-chr5:7886025..7888380,2	K562	blood:
2	chr5:7861753..7863633-chr5:7874321..7876476,2	K562	blood:
3	chr5:7874190..7876612-chr5:7884831..7887191,2	K562	blood:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs162027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162031	0.91[TSI][hapmap]
rs162032	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162037	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162038	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162040	0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs162045	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162048	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162130	1.00[YRI][hapmap]
rs2613670	0.89[TSI][hapmap]
rs2966952	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326119	0.87[ASN][1000 genomes]
rs326122	0.82[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs326124	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs49672	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs326120	MTRR	cis	Frontal Cortex	GTEx
rs326120	FASTKD3	cis	lymphoblastoid	seeQTL
rs326120	MTRR	cis	lymphoblastoid	seeQTL
rs326120	MTRR	cis	Lymphoblastoid	GTEx
rs326120	MTRR	cis	Temporal Cortex	GTEx
rs326120	MTRR	cis	Cerebellum	GTEx
rs326120	PAPD7	cis	cerebellum	SCAN
rs326120	MTRR	cis	Esophagus Muscularis	GTEx
rs326120	MTRR	cis	multi-tissue	Pritchard
rs326120	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870000-7875400	Weak transcription	Spleen	Spleen
2	chr5:7870200-7875400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:7870200-7875600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:7870200-7875600	Weak transcription	HSMMtube	muscle
5	chr5:7870200-7875800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:7870200-7875800	Weak transcription	Esophagus	oesophagus
7	chr5:7870200-7875800	Weak transcription	Gastric	stomach
8	chr5:7870200-7876000	Weak transcription	Fetal Brain Male	brain
9	chr5:7870200-7879800	Weak transcription	Pancreas	Pancrea
10	chr5:7870200-7882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:7870400-7875400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:7870400-7875600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:7870400-7875600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:7870600-7876200	Weak transcription	Fetal Stomach	stomach
16	chr5:7870600-7878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:7870600-7878400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:7870800-7875400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:7870800-7875600	Weak transcription	Fetal Brain Female	brain
20	chr5:7870800-7879800	Weak transcription	Colonic Mucosa	Colon
21	chr5:7871000-7875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:7871000-7875400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:7871000-7875400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:7871000-7875400	Weak transcription	HUVEC	blood vessel
25	chr5:7871000-7875400	Weak transcription	NH-A	brain
26	chr5:7871000-7875400	Weak transcription	NHLF	lung
27	chr5:7871000-7875600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:7871000-7875600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:7871000-7875600	Weak transcription	Ovary	ovary
30	chr5:7871000-7876000	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
32	chr5:7871200-7875400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:7871400-7877800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:7871400-7878000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr5:7871400-7902400	Strong transcription	K562	blood
39	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:7871600-7875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:7871600-7876600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
44	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
45	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:7871800-7875400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:7871800-7876800	Strong transcription	A549	lung

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