Variant report

Variant	rs724834
Chromosome Location	chr12:58180416-58180417
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58179133..58181417-chr12:58186670..58188914,2	MCF-7	breast:
2	chr12:58178480..58181770-chr12:58328004..58330583,3	K562	blood:
3	chr12:58179038..58181484-chr12:58333588..58335918,2	MCF-7	breast:
4	chr12:58179896..58182380-chr12:58239685..58241650,2	K562	blood:
5	chr12:58179045..58181481-chr12:58182237..58185060,2	K562	blood:
6	chr12:58179432..58181798-chr12:58197382..58199271,2	MCF-7	breast:
7	chr12:58179719..58182480-chr12:58197688..58200069,2	K562	blood:

Variant related genes	Relation type
ENSG00000166896	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000206749	Chromatin interaction
ENSG00000257698	Chromatin interaction
ENSG00000270039	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10431505	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783853	1.00[YRI][hapmap]
rs10877011	0.85[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10877012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172342	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172350	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.84[JPT][hapmap];0.85[YRI][hapmap]
rs11172371	0.85[YRI][hapmap]
rs1599931	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs1599932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875125	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2014886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2069506	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs4646536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs4760339	0.83[JPT][hapmap]
rs4760341	0.83[JPT][hapmap]
rs56177740	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs703842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652011	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs724834	METTL21B	cis	Heart Left Ventricle	GTEx
rs724834	FAM119B	cis	Frontal Cortex	GTEx
rs724834	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs724834	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs724834	METTL21B	cis	Muscle Skeletal	GTEx
rs724834	METTL21B	cis	Adipose Subcutaneous	GTEx
rs724834	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs724834	TSFM	cis	multi-tissue	Pritchard
rs724834	FAM119B	cis	Lymphoblastoid	GTEx
rs724834	CYP27B1	cis	Thyroid	GTEx
rs724834	METTL21B	cis	Whole Blood	GTEx
rs724834	DKFZP586D0919	cis	multi-tissue	Pritchard
rs724834	RP11-571M6.13	cis	Thyroid	GTEx
rs724834	METTL21B	cis	lung	GTEx
rs724834	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs724834	METTL21B	cis	Esophagus Muscularis	GTEx
rs724834	FAM119B	cis	Cerebellum	GTEx
rs724834	METTL21B	cis	Esophagus Mucosa	GTEx
rs724834	FAM119B	cis	Brain Pons	GTEx
rs724834	TSFM	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
2	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
5	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
6	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:58177600-58186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:58177800-58182600	Strong transcription	Placenta	Placenta
9	chr12:58177800-58184000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:58177800-58187400	Strong transcription	Osteobl	bone
11	chr12:58177800-58188400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:58177800-58189600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:58177800-58191200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:58177800-58192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:58178000-58181200	Strong transcription	NHDF-Ad	bronchial
19	chr12:58178000-58181400	Strong transcription	HSMM	muscle
20	chr12:58178000-58183800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:58178000-58184600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr12:58178000-58188600	Strong transcription	Fetal Lung	lung
23	chr12:58178000-58193200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:58178000-58194200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:58178000-58197200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:58178000-58197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:58178000-58198200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:58178000-58198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:58178000-58198200	Strong transcription	Fetal Thymus	thymus
30	chr12:58178200-58197000	Strong transcription	Fetal Intestine Large	intestine
31	chr12:58178200-58197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:58178200-58198200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:58178400-58184400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:58178400-58191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:58178400-58194000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:58178600-58181200	Strong transcription	Lung	lung
37	chr12:58178600-58182200	Strong transcription	K562	blood
38	chr12:58178600-58184200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:58178600-58187200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:58178600-58187400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:58178600-58187600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:58178600-58191400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:58178600-58207600	Strong transcription	Liver	Liver
44	chr12:58179000-58180600	Strong transcription	Brain Angular Gyrus	brain
45	chr12:58179000-58180600	Strong transcription	HepG2	liver
46	chr12:58179000-58181400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:58179000-58182000	Strong transcription	Fetal Brain Female	brain
48	chr12:58179000-58182000	Strong transcription	GM12878-XiMat	blood
49	chr12:58179000-58182400	Strong transcription	Primary B cells from cord blood	blood
50	chr12:58179000-58182600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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