Variant report

Variant	rs948358
Chromosome Location	chr11:66047523-66047524
allele	A/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	chr11:66047204-66047600	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:66047157-66047528	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:66047335-66048695	GM12891	blood:	n/a	n/a
4	REST	chr11:66044785-66047553	H1-neurons	neurons:	n/a	chr11:66045480-66045493 chr11:66047485-66047495 chr11:66045549-66045562
5	POLR2A	chr11:66047062-66051216	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66045260..66048745-chr11:66100560..66104011,3	K562	blood:
2	chr11:66047213..66049788-chr11:66097470..66100241,3	K562	blood:

Variant related genes	Relation type
CNIH2	TF binding region
ENSG00000254452	TF binding region
ENSG00000245156	TF binding region
ENSG00000174791	Chromatin interaction
ENSG00000254756	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1190945	0.86[AFR][1000 genomes]
rs1203551	0.86[AFR][1000 genomes]
rs1203552	0.86[AFR][1000 genomes]
rs1203801	1.00[YRI][hapmap]
rs1783732	1.00[YRI][hapmap]
rs2452687	1.00[YRI][hapmap]
rs3016315	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3017606	0.82[AFR][1000 genomes]
rs471203	1.00[MEX][hapmap]
rs471709	1.00[YRI][hapmap]
rs477001	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs505412	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs505642	1.00[YRI][hapmap]
rs510398	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs512316	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs515778	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs519911	1.00[YRI][hapmap]
rs527279	1.00[YRI][hapmap]
rs541954	1.00[YRI][hapmap]
rs547282	1.00[YRI][hapmap]
rs555527	1.00[YRI][hapmap]
rs555826	0.82[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs559298	1.00[YRI][hapmap]
rs561199	1.00[YRI][hapmap]
rs568423	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs571368	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs572697	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs581247	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv3438726	chr11:66042776-66047874	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv897777	chr11:66044882-66063654	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv897778	chr11:66044882-66066349	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv897779	chr11:66047523-66063654	Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs948358	LOC404266	trans	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66040800-66049600	Weak transcription	NHDF-Ad	bronchial
2	chr11:66042000-66055600	Weak transcription	Fetal Kidney	kidney
3	chr11:66042600-66048400	Weak transcription	A549	lung
4	chr11:66042800-66050200	Weak transcription	K562	blood
5	chr11:66043000-66050200	Weak transcription	Hela-S3	cervix
6	chr11:66044000-66047600	Weak transcription	HSMMtube	muscle
7	chr11:66044200-66048600	Weak transcription	NHLF	lung
8	chr11:66044200-66050200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:66044200-66051800	Weak transcription	Fetal Lung	lung
10	chr11:66045200-66047600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr11:66045400-66047800	Active TSS	Brain Hippocampus Middle	brain
12	chr11:66045400-66049200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:66045400-66050000	Weak transcription	Gastric	stomach
14	chr11:66045600-66049600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:66045600-66049600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:66045600-66049600	Weak transcription	GM12878-XiMat	blood
17	chr11:66045600-66050200	Weak transcription	Liver	Liver
18	chr11:66045600-66051800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:66045600-66051800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:66045600-66051800	Weak transcription	Esophagus	oesophagus
21	chr11:66045600-66052000	Weak transcription	Pancreas	Pancrea
22	chr11:66046000-66047800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:66046000-66049600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:66046000-66049800	Weak transcription	Left Ventricle	heart
25	chr11:66046000-66050800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:66046000-66052200	Weak transcription	HMEC	breast
27	chr11:66046000-66054000	Weak transcription	Aorta	Aorta
28	chr11:66046200-66047600	Weak transcription	HSMM	muscle
29	chr11:66046200-66050200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:66046400-66047600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:66046400-66047800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:66046400-66048000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:66046400-66048400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:66046400-66049200	Weak transcription	Right Ventricle	heart
35	chr11:66046400-66049400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:66046400-66049600	Weak transcription	Placenta	Placenta
37	chr11:66046400-66049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:66046400-66049600	Weak transcription	Dnd41	blood
39	chr11:66046400-66049800	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr11:66046400-66050000	Weak transcription	Ovary	ovary
41	chr11:66046400-66050200	Enhancers	Fetal Muscle Leg	muscle
42	chr11:66046600-66047600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr11:66046600-66047800	Flanking Active TSS	Fetal Brain Female	brain
44	chr11:66046600-66048000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:66046600-66048200	Bivalent Enhancer	Fetal Stomach	stomach
46	chr11:66046600-66049200	Weak transcription	Primary B cells from cord blood	blood
47	chr11:66046600-66049400	Weak transcription	Primary T cells from cord blood	blood
48	chr11:66046600-66052800	Weak transcription	Right Atrium	heart
49	chr11:66046800-66047600	Bivalent Enhancer	Fetal Intestine Small	intestine
50	chr11:66046800-66047600	Genic enhancers	Thymus	Thymus

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