Variant report

Variant	rs10877026
Chromosome Location	chr12:58229176-58229177
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58228216..58229792-chr12:58282546..58284939,2	K562	blood:
2	chr12:58145252..58148251-chr12:58228552..58230766,2	MCF-7	breast:
3	chr12:58228537..58230716-chr12:58295563..58297383,2	MCF-7	breast:
4	chr12:58227798..58230136-chr12:58279373..58282138,2	MCF-7	breast:
5	chr12:58219255..58221070-chr12:58228307..58230908,2	K562	blood:
6	chr12:58228517..58230592-chr12:58298078..58299845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000135446	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10444569	0.86[AMR][1000 genomes]
rs10747784	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783850	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783851	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783854	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783855	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783856	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10877024	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877025	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877029	0.82[AMR][1000 genomes]
rs10877030	0.82[AMR][1000 genomes]
rs10877031	0.86[AMR][1000 genomes]
rs10877032	0.81[AMR][1000 genomes]
rs11172361	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172362	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172367	0.81[AMR][1000 genomes]
rs11172369	0.82[AMR][1000 genomes]
rs12312955	0.83[AMR][1000 genomes]
rs12319233	0.83[AMR][1000 genomes]
rs12426201	0.86[AMR][1000 genomes]
rs1599750	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599751	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599931	0.85[AMR][1000 genomes]
rs1875125	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2002275	0.81[AMR][1000 genomes]
rs4237844	0.86[AMR][1000 genomes]
rs4760171	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4760172	0.82[AMR][1000 genomes]
rs4760332	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4760333	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4760335	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760339	0.86[AMR][1000 genomes]
rs4760341	0.83[AMR][1000 genomes]
rs5017863	0.85[AMR][1000 genomes]
rs7134797	0.82[AMR][1000 genomes]
rs7312623	0.86[AMR][1000 genomes]
rs7489290	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870392	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs871871	0.86[AMR][1000 genomes];0.99[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10877026	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877026	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877026	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877026	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877026	XRCC6BP1	cis	lung	GTEx
rs10877026	METTL21B	cis	Whole Blood	GTEx
rs10877026	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877026	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877026	METTL21B	cis	Muscle Skeletal	GTEx
rs10877026	XRCC6BP1	cis	Whole Blood	GTEx
rs10877026	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877026	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58222800-58230200	Enhancers	Right Atrium	heart
2	chr12:58222800-58230400	Genic enhancers	Fetal Stomach	stomach
3	chr12:58223000-58230400	Genic enhancers	Fetal Muscle Leg	muscle
4	chr12:58223400-58230400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:58223400-58231000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:58223400-58236400	Enhancers	Right Ventricle	heart
7	chr12:58223600-58230400	Weak transcription	Hela-S3	cervix
8	chr12:58223600-58231600	Enhancers	Placenta	Placenta
9	chr12:58223800-58230800	Enhancers	Liver	Liver
10	chr12:58224000-58230200	Weak transcription	Dnd41	blood
11	chr12:58224200-58230600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:58224200-58238200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:58224400-58238000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:58224400-58238200	Enhancers	Spleen	Spleen
15	chr12:58224800-58229600	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:58225000-58230200	Enhancers	Fetal Heart	heart
17	chr12:58225200-58237000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:58225400-58235600	Genic enhancers	Fetal Intestine Small	intestine
19	chr12:58225600-58229800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:58225600-58232800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:58225600-58238200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:58225800-58229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:58225800-58229200	Enhancers	Primary T cells from cord blood	blood
24	chr12:58225800-58229200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:58225800-58229400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:58225800-58229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:58225800-58229400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:58225800-58229400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:58225800-58229400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:58225800-58229600	Enhancers	Primary hematopoietic stem cells	blood
31	chr12:58225800-58229600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr12:58225800-58229800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr12:58225800-58229800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr12:58225800-58230000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:58225800-58230400	Weak transcription	A549	lung
36	chr12:58225800-58230600	Enhancers	Thymus	Thymus
37	chr12:58225800-58236000	Enhancers	Brain Angular Gyrus	brain
38	chr12:58226000-58229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:58226000-58229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:58226000-58229200	Enhancers	Adipose Nuclei	Adipose
41	chr12:58226000-58229200	Enhancers	NHLF	lung
42	chr12:58226000-58229400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:58226000-58229400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:58226000-58229400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:58226000-58229400	Enhancers	Colonic Mucosa	Colon
46	chr12:58226000-58229400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr12:58226000-58229400	Weak transcription	HMEC	breast
48	chr12:58226000-58229400	Weak transcription	NHEK	skin
49	chr12:58226000-58229600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:58226000-58229600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links