Variant report

Variant	rs2509943
Chromosome Location	chr11:94231257-94231258
allele	C/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	chr11:94231099-94231733	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:94231239-94231315	K562	blood:	n/a	n/a
3	POLR2A	chr11:94230649-94231398	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:94225979..94229384-chr11:94230397..94235421,9	K562	blood:
2	chr11:94227017..94228715-chr11:94231164..94232764,2	MCF-7	breast:
3	chr11:94150497..94152449-chr11:94231090..94232947,2	K562	blood:

Variant related genes	Relation type
MRE11A	TF binding region
ENSG00000020922	Chromatin interaction
ENSG00000168876	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1014666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11020799	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1270146	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508460	0.80[AMR][1000 genomes]
rs2508784	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2509321	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2509324	0.84[AMR][1000 genomes]
rs4342993	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4593974	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs472344	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473297	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475531	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs476137	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs482629	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs486556	0.82[EUR][1000 genomes]
rs489200	0.81[EUR][1000 genomes]
rs492001	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs493982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs496190	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs496797	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs500558	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524350	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525057	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs525921	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs536768	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs544337	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs547207	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs553634	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs557148	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs569143	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs582049	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs582077	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs610899	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs612075	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs612632	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs614424	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs621562	0.86[EUR][1000 genomes]
rs622961	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs628079	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs628164	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs628728	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs629119	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs629156	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs642744	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs647249	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6483341	0.88[EUR][1000 genomes]
rs659349	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs662572	0.84[EUR][1000 genomes]
rs682213	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs684507	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693815	0.83[AMR][1000 genomes]

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2509943	RP11-685N10.1	cis	Nerve Tibial	GTEx
rs2509943	MRE11A	Cis_1M	lymphoblastoid	RTeQTL
rs2509943	RP11-685N10.1	cis	lung	GTEx
rs2509943	MRE11A	cis	Stomach	GTEx
rs2509943	RP11-685N10.1	cis	Heart Left Ventricle	GTEx
rs2509943	MRE11A	cis	lung	GTEx
rs2509943	MRE11A	cis	Esophagus Muscularis	GTEx
rs2509943	MRE11A	cis	Skin Sun Exposed Lower leg	GTEx
rs2509943	MRE11A	cis	Adipose Subcutaneous	GTEx
rs2509943	RP11-685N10.1	cis	Esophagus Muscularis	GTEx
rs2509943	RP11-685N10.1	cis	Stomach	GTEx
rs2509943	MRE11A	cis	Esophagus Mucosa	GTEx
rs2509943	MRE11A	cis	Thyroid	GTEx
rs2509943	MRE11A	cis	Heart Left Ventricle	GTEx
rs2509943	RP11-685N10.1	cis	Artery Tibial	GTEx
rs2509943	MRE11A	cis	Artery Tibial	GTEx
rs2509943	MRE11A	cis	Nerve Tibial	GTEx
rs2509943	RP11-685N10.1	cis	Artery Aorta	GTEx
rs2509943	RP11-685N10.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2509943	RP11-685N10.1	cis	Esophagus Mucosa	GTEx
rs2509943	RP11-685N10.1	cis	Thyroid	GTEx
rs2509943	RP11-685N10.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94227600-94233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:94227600-94234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:94227800-94231800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:94227800-94232800	Weak transcription	Spleen	Spleen
5	chr11:94227800-94235400	Weak transcription	Pancreas	Pancrea
6	chr11:94227800-94236400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:94227800-94237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:94227800-94237000	Weak transcription	Aorta	Aorta
9	chr11:94227800-94238400	Weak transcription	Small Intestine	intestine
10	chr11:94227800-94238800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:94227800-94245200	Weak transcription	Gastric	stomach
12	chr11:94228000-94232000	Weak transcription	Psoas Muscle	Psoas
13	chr11:94228000-94235400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:94228000-94245000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:94228000-94245200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:94228000-94245800	Weak transcription	Stomach Mucosa	stomach
17	chr11:94228200-94232000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:94228400-94245200	Weak transcription	Fetal Stomach	stomach
19	chr11:94228600-94232200	Weak transcription	Fetal Heart	heart
20	chr11:94228600-94233000	Weak transcription	Brain Germinal Matrix	brain
21	chr11:94228600-94233800	Weak transcription	Fetal Intestine Small	intestine
22	chr11:94228600-94235200	Weak transcription	A549	lung
23	chr11:94229000-94232200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:94229200-94232200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:94229200-94232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:94229200-94232600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:94229200-94233600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:94229200-94233600	Strong transcription	Dnd41	blood
29	chr11:94229600-94232600	Strong transcription	GM12878-XiMat	blood
30	chr11:94229600-94233600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:94229600-94235600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:94229800-94232000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:94229800-94232400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:94229800-94232600	Strong transcription	NH-A	brain
35	chr11:94229800-94232600	Strong transcription	Osteobl	bone
36	chr11:94229800-94233600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:94229800-94233800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:94229800-94234000	Strong transcription	Fetal Thymus	thymus
39	chr11:94229800-94234200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:94229800-94234200	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:94229800-94234200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr11:94229800-94234400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:94229800-94234400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:94229800-94234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:94229800-94235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:94229800-94235200	Strong transcription	Liver	Liver
47	chr11:94229800-94235400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:94229800-94235400	Strong transcription	Primary T cells from cord blood	blood
49	chr11:94229800-94235400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr11:94229800-94235400	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links