Variant report

Variant	rs162037
Chromosome Location	chr5:7886104-7886105
allele	C/T
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	chr5:7884366-7886330	K562	blood:	n/a	n/a
2	CTCF	chr5:7886020-7886170	GM12873	blood:	n/a	n/a
3	POLR2A	chr5:7885866-7886241	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr5:7886052-7886118	ProgFib	skin:	n/a	n/a
5	POLR2A	chr5:7886030-7886131	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:7866975..7869850-chr5:7885041..7887303,3	K562	blood:
2	chr5:7874190..7876612-chr5:7884831..7887191,2	K562	blood:
3	chr5:7873979..7876833-chr5:7886025..7888380,2	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs162027	0.88[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs162030	0.89[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162031	0.97[TSI][hapmap]
rs162032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162040	0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs162045	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162048	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162049	0.81[EUR][1000 genomes]
rs162130	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162270	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162272	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162273	0.83[EUR][1000 genomes]
rs162448	0.80[CHB][hapmap]
rs16879452	0.83[ASN][1000 genomes]
rs1826541	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1994866	0.84[ASN][1000 genomes]
rs2077744	0.90[JPT][hapmap]
rs2613663	0.82[ASN][1000 genomes]
rs2613670	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624228	0.82[ASN][1000 genomes]
rs2624229	0.82[ASN][1000 genomes]
rs2624230	0.82[ASN][1000 genomes]
rs2624231	0.82[ASN][1000 genomes]
rs2624237	0.89[JPT][hapmap]
rs2640664	0.82[ASN][1000 genomes]
rs2640665	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2966952	0.96[GIH][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs326120	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]
rs326122	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs326124	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs327573	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs327575	0.90[JPT][hapmap]
rs327582	0.85[ASN][1000 genomes]
rs329831	0.82[CHD][hapmap]
rs49672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs162037	MTRR	cis	Esophagus Muscularis	GTEx
rs162037	MTRR	cis	Brain Pons	GTEx
rs162037	MTRR	cis	lymphoblastoid	seeQTL
rs162037	MTRR	cis	Temporal Cortex	GTEx
rs162037	PAPD7	cis	cerebellum	SCAN
rs162037	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs162037	MTRR	cis	Frontal Cortex	GTEx
rs162037	MTRR	cis	Lymphoblastoid	GTEx
rs162037	MTRR	cis	Cerebellum	GTEx
rs162037	MTRR	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
3	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:7871400-7902400	Strong transcription	K562	blood
7	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
10	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
11	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
18	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:7873200-7903400	Strong transcription	Dnd41	blood
21	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
22	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
24	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
27	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:7875400-7886200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:7875400-7887200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:7875400-7887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr5:7875600-7886200	Strong transcription	Ovary	ovary
39	chr5:7875600-7886200	Strong transcription	Thymus	Thymus
40	chr5:7875600-7886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:7875600-7887200	Strong transcription	Fetal Brain Female	brain
42	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
43	chr5:7877600-7886200	Strong transcription	Fetal Stomach	stomach
44	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr5:7878800-7887400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr5:7878800-7888600	Weak transcription	Psoas Muscle	Psoas
47	chr5:7878800-7890600	Strong transcription	NH-A	brain
48	chr5:7879000-7886200	Strong transcription	NHLF	lung
49	chr5:7879000-7887000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:7879000-7887200	Strong transcription	HSMM	muscle

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