Variant report

Variant	rs2412344
Chromosome Location	chr11:4107584-4107585
allele	C/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	POLR2A	chr11:4105709-4107655	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3861564..3863892-chr11:4106134..4108924,2	MCF-7	breast:

Variant related genes	Relation type
STIM1	TF binding region
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10742223	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10767807	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10835613	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs10835632	0.82[EUR][1000 genomes]
rs10835650	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11030853	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030967	0.81[EUR][1000 genomes]
rs11030976	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11604649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12292367	0.81[EUR][1000 genomes]
rs12364664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12799265	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12803023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1372805	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1662172	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119986	0.82[EUR][1000 genomes]
rs2304891	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920139	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2920143	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2920144	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2923953	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2959066	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2959068	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959074	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2959079	0.81[AMR][1000 genomes]
rs2959081	0.82[CHB][hapmap]
rs54816	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7102508	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7110060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7116520	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124301	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs725518	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs725519	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs747883	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9704047	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[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	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
3	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
4	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
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412344	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
2	chr11:4070800-4108600	Weak transcription	HSMM	muscle
3	chr11:4079000-4112600	Weak transcription	Fetal Brain Female	brain
4	chr11:4086200-4115200	Weak transcription	NHDF-Ad	bronchial
5	chr11:4087600-4115000	Weak transcription	HSMMtube	muscle
6	chr11:4087800-4107800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:4088600-4107800	Weak transcription	Right Ventricle	heart
8	chr11:4091600-4107600	Weak transcription	Psoas Muscle	Psoas
9	chr11:4093600-4112600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:4093800-4115000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:4093800-4115200	Weak transcription	Fetal Kidney	kidney
12	chr11:4094000-4107800	Weak transcription	Brain Angular Gyrus	brain
13	chr11:4094000-4108600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:4094000-4108600	Weak transcription	Osteobl	bone
15	chr11:4094000-4115000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:4094000-4115000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:4094000-4115200	Weak transcription	Brain Substantia Nigra	brain
18	chr11:4095800-4109400	Weak transcription	K562	blood
19	chr11:4096000-4107600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:4098200-4115000	Weak transcription	Hela-S3	cervix
21	chr11:4099400-4107800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:4099400-4111200	Strong transcription	Fetal Thymus	thymus
23	chr11:4100200-4115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:4100400-4110400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:4100600-4115200	Weak transcription	NHLF	lung
26	chr11:4101000-4110600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:4101400-4108000	Strong transcription	Primary T cells from cord blood	blood
28	chr11:4101400-4112800	Strong transcription	Thymus	Thymus
29	chr11:4101400-4113600	Strong transcription	Primary B cells from cord blood	blood
30	chr11:4101400-4114000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:4101400-4114200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr11:4101600-4113200	Strong transcription	Dnd41	blood
33	chr11:4101600-4113800	Strong transcription	Adipose Nuclei	Adipose
34	chr11:4101800-4108000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:4101800-4108400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:4101800-4112000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:4101800-4113400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:4101800-4114000	Strong transcription	Fetal Stomach	stomach
39	chr11:4102000-4108400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:4102000-4113200	Strong transcription	Liver	Liver
41	chr11:4102200-4108000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:4102200-4109800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:4102200-4114000	Strong transcription	Spleen	Spleen
44	chr11:4102400-4107800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:4102400-4110200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:4102400-4113400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:4102400-4115200	Weak transcription	Fetal Brain Male	brain
48	chr11:4102800-4108400	Strong transcription	Esophagus	oesophagus
49	chr11:4102800-4109000	Strong transcription	Left Ventricle	heart
50	chr11:4102800-4110000	Strong transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links