Variant report

Variant	rs2920139
Chromosome Location	chr11:4083716-4083717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:4082609..4084818-chr11:4091785..4094735,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10742223	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10767807	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11030394	0.91[AFR][1000 genomes]
rs11030536	0.85[AFR][1000 genomes]
rs11030853	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11030907	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11604649	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12364664	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12419208	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12799265	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12803023	0.86[ASN][1000 genomes]
rs1372804	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1372805	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304891	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412344	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2920143	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2920144	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2923944	0.91[AFR][1000 genomes]
rs2923950	0.80[EUR][1000 genomes]
rs2923953	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2958713	0.87[AFR][1000 genomes]
rs2958714	0.91[AFR][1000 genomes]
rs2959065	0.83[AMR][1000 genomes]
rs2959066	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2959068	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2959070	0.81[ASN][1000 genomes]
rs2959074	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959079	0.80[AMR][1000 genomes]
rs7102508	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7110060	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7116520	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7124301	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747883	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9704047	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920139	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
3	chr11:4066600-4085800	Weak transcription	Pancreas	Pancrea
4	chr11:4067000-4087400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:4067800-4093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:4070800-4108600	Weak transcription	HSMM	muscle
7	chr11:4073000-4093200	Weak transcription	Fetal Intestine Small	intestine
8	chr11:4076000-4087000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:4076200-4103000	Weak transcription	Fetal Intestine Large	intestine
10	chr11:4076600-4085200	Strong transcription	Dnd41	blood
11	chr11:4078000-4093200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:4078800-4084400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:4079000-4093000	Weak transcription	Brain Germinal Matrix	brain
14	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
15	chr11:4079200-4085200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr11:4079400-4085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:4079400-4085800	Weak transcription	Fetal Heart	heart
18	chr11:4079600-4083800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:4079600-4087200	Weak transcription	NH-A	brain
20	chr11:4079800-4084600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:4079800-4085800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:4079800-4093200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:4080000-4084400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:4080000-4086200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:4080200-4088000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:4080400-4085400	Strong transcription	Primary B cells from cord blood	blood
27	chr11:4080400-4087800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:4080600-4084200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:4080800-4084200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr11:4081000-4085800	Weak transcription	Right Ventricle	heart
31	chr11:4081000-4089800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:4081000-4090000	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:4081000-4090000	Weak transcription	Esophagus	oesophagus
34	chr11:4081000-4101800	Weak transcription	Lung	lung
35	chr11:4081000-4104600	Weak transcription	Colonic Mucosa	Colon
36	chr11:4081200-4093000	Weak transcription	Fetal Kidney	kidney
37	chr11:4081200-4095400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:4081400-4095600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:4081600-4085600	Weak transcription	Gastric	stomach
40	chr11:4081600-4086000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:4081600-4086400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:4081600-4092800	Weak transcription	Fetal Stomach	stomach
43	chr11:4081800-4084800	Weak transcription	NHLF	lung
44	chr11:4081800-4085400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:4081800-4085800	Weak transcription	Left Ventricle	heart
46	chr11:4081800-4095200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:4081800-4095600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:4082000-4083800	Weak transcription	NHEK	skin
49	chr11:4082000-4085800	Weak transcription	Aorta	Aorta
50	chr11:4082000-4085800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links