Variant report

Variant	rs2966952
Chromosome Location	chr5:7868030-7868031
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	IRF1	chr5:7867988-7869519	K562	blood:	n/a	chr5:7868801-7868815
2	MXI1	chr5:7867903-7870446	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:6632601..6634168-chr5:7866506..7869166,2	K562	blood:
2	chr5:7867721..7870602-chr5:7899852..7901700,2	MCF-7	breast:
3	chr5:7867651..7870301-chr5:7886397..7888680,2	MCF-7	breast:
4	chr5:7866975..7869850-chr5:7885041..7887303,3	K562	blood:
5	chr5:7867976..7870362-chr5:7899262..7901515,2	K562	blood:

Variant related genes	Relation type
FASTKD3	TF binding region
MTRR	TF binding region
ENSG00000124275	Chromatin interaction
ENSG00000037474	Chromatin interaction
ENSG00000145545	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs162027	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162030	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162031	0.80[TSI][hapmap]
rs162032	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162037	0.96[GIH][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162038	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162045	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162048	0.96[GIH][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162130	1.00[YRI][hapmap]
rs326119	0.87[ASN][1000 genomes]
rs326120	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]
rs326124	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs49672	0.80[AMR][1000 genomes];0.86[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2966952	MTRR	cis	multi-tissue	Pritchard
rs2966952	MTRR	cis	lymphoblastoid	seeQTL
rs2966952	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs2966952	MTRR	cis	Frontal Cortex	GTEx
rs2966952	MTRR	cis	Cerebellum	GTEx
rs2966952	MTRR	cis	Esophagus Muscularis	GTEx
rs2966952	MTRR	cis	Temporal Cortex	GTEx
rs2966952	FASTKD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:7852200-7868400	Weak transcription	Gastric	stomach
5	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:7852800-7868400	Weak transcription	Pancreas	Pancrea
7	chr5:7854000-7868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:7856000-7868400	Weak transcription	Stomach Mucosa	stomach
9	chr5:7858400-7868200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:7858800-7868400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:7860400-7868400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:7862400-7868200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:7862800-7868400	Weak transcription	Aorta	Aorta
14	chr5:7863000-7868400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:7863000-7868400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:7863000-7868400	Weak transcription	Colonic Mucosa	Colon
17	chr5:7863000-7868400	Weak transcription	HSMMtube	muscle
18	chr5:7863200-7868200	Weak transcription	Psoas Muscle	Psoas
19	chr5:7863200-7868400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:7864400-7868200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:7865200-7868600	Weak transcription	Small Intestine	intestine
22	chr5:7865800-7868400	Enhancers	Fetal Intestine Small	intestine
23	chr5:7866000-7868200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr5:7866000-7868400	Weak transcription	Placenta	Placenta
25	chr5:7866200-7868400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:7866200-7868400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr5:7866400-7868200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr5:7866400-7868400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:7866600-7868200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:7866600-7868400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:7866800-7868200	Enhancers	Primary T cells from cord blood	blood
32	chr5:7866800-7868200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:7867000-7868200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr5:7867000-7868400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:7867000-7868400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:7867200-7868200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:7867400-7868200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr5:7867400-7868200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:7867400-7868200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:7867400-7868200	Enhancers	Brain Cingulate Gyrus	brain
41	chr5:7867400-7868200	Enhancers	Colon Smooth Muscle	Colon
42	chr5:7867400-7868400	Enhancers	Left Ventricle	heart
43	chr5:7867600-7868200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:7867600-7868200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr5:7867600-7868200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr5:7867600-7868200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr5:7867600-7868200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr5:7867600-7868200	Flanking Active TSS	HepG2	liver
49	chr5:7867600-7868400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:7867600-7868400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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