Variant report

Variant	rs10831239
Chromosome Location	chr11:94276209-94276210
allele	G/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	RELA	chr11:94276144-94277715	GM19193	blood:	n/a	chr11:94276320-94276329 chr11:94276320-94276329
2	RELA	chr11:94276139-94277472	GM19099	blood:	n/a	chr11:94276320-94276329 chr11:94276320-94276329
3	POLR2A	chr11:94276155-94277714	GM12891	blood:	n/a	n/a
4	RELA	chr11:94276170-94276993	GM12878	blood:	n/a	chr11:94276320-94276329 chr11:94276320-94276329
5	RELA	chr11:94276175-94277787	GM18951	blood:	n/a	chr11:94276320-94276329 chr11:94276320-94276329
6	POLR2A	chr11:94276074-94277866	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:94276052-94281337	HL-60	blood:	n/a	n/a
8	RELA	chr11:94276103-94277920	GM12891	blood:	n/a	chr11:94276320-94276329 chr11:94276320-94276329
9	MAZ	chr11:94276201-94276467	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:94273988..94276726-chr11:94311479..94314894,4	K562	blood:
2	chr11:94273509..94276293-chr11:94301619..94303919,2	K562	blood:
3	chr11:94225466..94228271-chr11:94275709..94278301,3	K562	blood:
4	chr11:94226771..94229140-chr11:94275887..94279295,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRE11A-3	chr11:94276131-94277949	NONHSAT023724
2	lnc-MRE11A-3	chr11:94275325-94277016	NONHSAT023723

Variant related genes	Relation type
FUT4	TF binding region
PIWIL4	TF binding region
ENSG00000020922	Chromatin interaction
ENSG00000168876	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10741490	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11020832	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11020851	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs1257380	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs591584	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs6483346	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7926082	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926234	0.80[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs7927312	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927463	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7929056	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7946385	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7946916	0.82[EUR][1000 genomes]
rs7950626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9919636	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10831239	C11orf54	cis	cerebellum	SCAN
rs10831239	PIWIL4	cis	lymphoblastoid	seeQTL
rs10831239	MED17	cis	parietal	SCAN
rs10831239	MED17	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94267600-94276400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:94270600-94276400	Weak transcription	Fetal Lung	lung
3	chr11:94271000-94276400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr11:94271200-94276400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:94271200-94276400	Weak transcription	Adipose Nuclei	Adipose
6	chr11:94271200-94276600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:94271200-94276800	Weak transcription	HMEC	breast
8	chr11:94272400-94276400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr11:94272600-94276800	Weak transcription	Small Intestine	intestine
10	chr11:94275000-94276400	Enhancers	Fetal Intestine Small	intestine
11	chr11:94275200-94276400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:94275400-94276800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:94275600-94276400	Enhancers	Colonic Mucosa	Colon
14	chr11:94275800-94276600	Enhancers	Stomach Mucosa	stomach
15	chr11:94276000-94276400	Enhancers	Fetal Intestine Large	intestine
16	chr11:94276000-94276600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr11:94276000-94276600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:94276200-94276400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:94276200-94276400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:94276200-94276400	Enhancers	Primary B cells from cord blood	blood
21	chr11:94276200-94276400	Enhancers	Primary T cells from cord blood	blood
22	chr11:94276200-94276400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:94276200-94276400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:94276200-94276400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr11:94276200-94276400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:94276200-94276400	Enhancers	Brain Cingulate Gyrus	brain
27	chr11:94276200-94276400	Enhancers	Brain Hippocampus Middle	brain
28	chr11:94276200-94276400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr11:94276200-94276400	Enhancers	Colon Smooth Muscle	Colon
30	chr11:94276200-94276400	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:94276200-94276400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr11:94276200-94276400	Enhancers	Fetal Kidney	kidney
33	chr11:94276200-94276400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr11:94276200-94276400	Enhancers	GM12878-XiMat	blood
35	chr11:94276200-94276600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr11:94276200-94276600	Enhancers	Primary hematopoietic stem cells	blood
37	chr11:94276200-94276600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:94276200-94276600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr11:94276200-94276600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr11:94276200-94276600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:94276200-94276600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr11:94276200-94276600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:94276200-94276600	Enhancers	Aorta	Aorta
44	chr11:94276200-94276600	Enhancers	Brain Angular Gyrus	brain
45	chr11:94276200-94276600	Enhancers	Fetal Thymus	thymus
46	chr11:94276200-94276600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr11:94276200-94276600	Enhancers	Thymus	Thymus
48	chr11:94276200-94276600	Flanking Active TSS	A549	lung
49	chr11:94276200-94276800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:94276200-94276800	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links