Variant report

Variant	rs10877017
Chromosome Location	chr12:58169361-58169362
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	SPI1	chr12:58169299-58169800	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58169310..58172664-chr12:58174820..58180538,7	MCF-7	breast:
2	chr12:58168432..58170962-chr12:58239519..58241035,2	K562	blood:
3	chr12:57912814..57915992-chr12:58164344..58170030,6	K562	blood:

Variant related genes	Relation type
ENSG00000266465	TF binding region
METTL1	TF binding region
ENSG00000123297	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1021469	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10431505	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10431552	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747783	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783847	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783848	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877011	0.83[EUR][1000 genomes]
rs10877012	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877013	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877014	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877015	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877018	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877019	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172333	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172335	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172342	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172343	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172344	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172349	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172350	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172351	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599932	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1875124	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014886	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069502	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069506	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072052	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291617	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782130	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825079	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646536	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56177740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs703842	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724834	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965287	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8181644	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923829	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9652011	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10877017	METTL21B	cis	Adipose Subcutaneous	GTEx
rs10877017	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs10877017	METTL21B	cis	Nerve Tibial	GTEx
rs10877017	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877017	METTL21B	cis	Whole Blood	GTEx
rs10877017	XRCC6BP1	cis	Whole Blood	GTEx
rs10877017	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10877017	TSFM	cis	Muscle Skeletal	GTEx
rs10877017	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877017	METTL21B	cis	Heart Left Ventricle	GTEx
rs10877017	METTL21B	cis	Esophagus Mucosa	GTEx
rs10877017	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877017	METTL21B	cis	lung	GTEx
rs10877017	METTL21B	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58166800-58176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:58167000-58169400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:58167000-58172400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:58167000-58173600	Weak transcription	Brain Anterior Caudate	brain
5	chr12:58167000-58173600	Weak transcription	Esophagus	oesophagus
6	chr12:58167000-58174000	Weak transcription	Aorta	Aorta
7	chr12:58167000-58175600	Weak transcription	Spleen	Spleen
8	chr12:58167000-58175800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:58167000-58176400	Weak transcription	Gastric	stomach
10	chr12:58167200-58169400	Weak transcription	A549	lung
11	chr12:58167200-58171800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:58167200-58172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:58167200-58173600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:58167200-58173800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:58167200-58174000	Weak transcription	Primary T cells from cord blood	blood
16	chr12:58167200-58174000	Weak transcription	Brain Germinal Matrix	brain
17	chr12:58167200-58174000	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:58167200-58174200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:58167200-58174200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:58167200-58174400	Weak transcription	Liver	Liver
21	chr12:58167200-58174600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:58167200-58175600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:58167200-58176000	Weak transcription	Brain Angular Gyrus	brain
24	chr12:58167200-58176000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:58167200-58176400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:58167200-58176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:58167200-58176400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:58167200-58176400	Weak transcription	Right Ventricle	heart
29	chr12:58167400-58169400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:58167400-58170000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:58167400-58170800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:58167400-58175600	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:58167400-58175600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:58167400-58176000	Weak transcription	Fetal Intestine Large	intestine
35	chr12:58167400-58176200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:58167400-58176200	Weak transcription	Brain Substantia Nigra	brain
37	chr12:58167400-58176400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:58167400-58176400	Weak transcription	Colonic Mucosa	Colon
39	chr12:58167400-58176400	Weak transcription	Left Ventricle	heart
40	chr12:58167600-58169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:58167600-58169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:58167600-58169400	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:58167600-58169400	Weak transcription	HSMM	muscle
44	chr12:58167600-58169400	Weak transcription	NHEK	skin
45	chr12:58167600-58169600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:58167600-58170000	Weak transcription	NHLF	lung
47	chr12:58167600-58170400	Weak transcription	Small Intestine	intestine
48	chr12:58167600-58171400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:58167600-58172000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:58167600-58173400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links