Variant report

Variant	rs11172350
Chromosome Location	chr12:58213272-58213273
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	chr12:58210243-58213716	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:58212188-58213594	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:58212030-58219642	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:58209632-58221838	K562	blood:	n/a	n/a
5	FOSL2	chr12:58210992-58213277	HepG2	liver:	n/a	chr12:58212588-58212597

No.	Distal block	Cell Line	Cell type
1	chr12:58212086..58214984-chr12:58238632..58241452,2	K562	blood:
2	chr12:58212873..58215210-chr12:58216073..58217617,2	MCF-7	breast:
3	chr12:58211567..58213701-chr12:58218722..58220729,2	MCF-7	breast:
4	chr12:58209123..58211135-chr12:58212326..58215029,2	MCF-7	breast:
5	chr12:58206978..58209497-chr12:58211355..58214120,3	K562	blood:

Variant related genes	Relation type
AVIL	TF binding region
ENSG00000175215	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000269903	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs1021469	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10431505	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431552	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10747783	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783847	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783848	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877011	0.81[EUR][1000 genomes]
rs10877012	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877013	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10877014	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877015	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877016	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877017	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877018	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877019	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172333	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172335	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172342	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172343	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172344	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172349	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172351	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599932	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875124	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2014886	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2069502	0.91[EUR][1000 genomes]
rs2069506	0.89[EUR][1000 genomes]
rs2072052	0.91[EUR][1000 genomes]
rs2291617	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3782130	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825079	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4646536	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56177740	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs703842	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs724834	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7965287	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8181644	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs923829	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9652011	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11172350	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs11172350	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs11172350	METTL21B	cis	Adipose Subcutaneous	GTEx
rs11172350	TSFM	cis	Muscle Skeletal	GTEx
rs11172350	METTL21B	cis	lung	GTEx
rs11172350	XRCC6BP1	cis	Whole Blood	GTEx
rs11172350	METTL21B	cis	Muscle Skeletal	GTEx
rs11172350	METTL21B	cis	Esophagus Mucosa	GTEx
rs11172350	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs11172350	METTL21B	cis	Esophagus Muscularis	GTEx
rs11172350	METTL21B	cis	Whole Blood	GTEx
rs11172350	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172350	METTL21B	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
3	chr12:58187000-58216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:58187200-58215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:58190200-58216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:58190800-58215200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:58190800-58216200	Weak transcription	HUVEC	blood vessel
8	chr12:58191000-58216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:58191200-58213600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:58191200-58216200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:58192200-58216200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:58193200-58215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:58193400-58216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:58194200-58215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:58197200-58216400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:58198400-58215000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:58201200-58215000	Weak transcription	Fetal Kidney	kidney
18	chr12:58202400-58214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:58202400-58215000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:58202400-58215200	Weak transcription	GM12878-XiMat	blood
21	chr12:58202600-58214400	Weak transcription	Dnd41	blood
22	chr12:58203200-58213600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:58203400-58216600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:58203800-58214400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:58204200-58214000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:58204200-58216400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:58204600-58214800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:58204800-58216200	Weak transcription	NHEK	skin
29	chr12:58205000-58213400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:58205000-58216600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:58205000-58216600	Weak transcription	Hela-S3	cervix
32	chr12:58205200-58213400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:58205200-58213400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:58205200-58214200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:58205400-58213400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:58207400-58214400	Weak transcription	Primary T cells from cord blood	blood
37	chr12:58207400-58215000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:58207800-58222800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:58208600-58215400	Enhancers	HepG2	liver
40	chr12:58208800-58213400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:58209200-58213600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:58209400-58216400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:58209600-58216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:58209800-58213800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:58210000-58213400	Weak transcription	Pancreas	Pancrea
47	chr12:58210000-58213600	Weak transcription	Esophagus	oesophagus
48	chr12:58210200-58213400	Weak transcription	Spleen	Spleen
49	chr12:58210800-58213400	Weak transcription	Gastric	stomach
50	chr12:58210800-58217000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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