Variant report

Variant	rs505412
Chromosome Location	chr11:66018155-66018156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66017903-66018630	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:66017701-66019063	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:66017910-66018623	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:66018083-66018440	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:66017088-66018734	GM12892	blood:	n/a	n/a
6	POLR2A	chr11:66017210-66018653	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:66018029-66018411	MCF-7	breast:	n/a	n/a
8	POLR2A	chr11:66017187-66018679	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr11:66018082-66018350	K562	blood:	n/a	n/a
10	POLR2A	chr11:66018007-66018353	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:66017974-66018441	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:66017938-66018431	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:66017946-66018484	GM12892	blood:	n/a	n/a
14	GATA3	chr11:66018064-66018301	SH-SY5Y	brain:	n/a	n/a
15	POLR2A	chr11:66017879-66018533	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr11:66017131-66018624	GM12892	blood:	n/a	n/a
17	POLR2A	chr11:66018077-66018178	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr11:66016211-66018687	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:66017920-66018477	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:66018112-66018197	K562	blood:	n/a	n/a
21	GATA2	chr11:66017980-66018408	SH-SY5Y	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66016483..66019098-chr11:66034608..66037453,2	K562	blood:
2	chr11:66015001..66021164-chr11:66021602..66026109,13	K562	blood:
3	chr11:66017102..66019513-chr11:66024628..66027866,4	MCF-7	breast:
4	chr11:66014122..66016479-chr11:66016572..66018624,2	MCF-7	breast:
5	chr11:66017033..66019908-chr11:66028745..66031527,2	K562	blood:
6	chr11:66008820..66013375-chr11:66014449..66019196,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255320	TF binding region
ENSG00000174996	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000174903	Chromatin interaction
ENSG00000254461	Chromatin interaction
ENSG00000254762	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1151532	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1191715	0.88[AFR][1000 genomes]
rs1203551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203750	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203801	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1300706	0.81[AFR][1000 genomes]
rs1630638	0.88[AFR][1000 genomes]
rs1783562	0.85[AFR][1000 genomes]
rs1783732	1.00[YRI][hapmap]
rs2430981	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2452687	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016315	0.92[AFR][1000 genomes]
rs3017606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs471203	1.00[MEX][hapmap]
rs471709	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs477001	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs485547	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4930332	0.89[AFR][1000 genomes]
rs502898	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs504456	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505642	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs510398	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs512316	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs515778	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519911	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527279	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs541954	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs547282	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs547892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs549228	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs551652	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs555527	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs555826	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs559298	0.84[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs560105	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561199	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561869	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs567414	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs568423	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs571368	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs572697	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs577301	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs581247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6591196	0.85[AFR][1000 genomes]
rs693382	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7934588	0.82[AFR][1000 genomes]
rs7947668	0.88[AFR][1000 genomes]
rs948358	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]
rs948477	0.88[AFR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs505412	LOC404266	trans	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:65989600-66024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:65990200-66019800	Strong transcription	Primary T cells from cord blood	blood
5	chr11:65990600-66018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:65990800-66018600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr11:65991200-66018600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:65991200-66018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:65991600-66018400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:65991600-66018400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:65991800-66018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:65993800-66018400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr11:65994400-66018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:65994600-66018600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:65995000-66018800	Strong transcription	Fetal Intestine Small	intestine
16	chr11:65996000-66024400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:65997400-66018600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:65997600-66018400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:65998000-66018600	Strong transcription	Fetal Brain Female	brain
20	chr11:65999800-66024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:66000800-66024200	Weak transcription	HMEC	breast
22	chr11:66001600-66024200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:66002000-66021000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:66003400-66024200	Weak transcription	HepG2	liver
25	chr11:66003400-66024200	Weak transcription	NHDF-Ad	bronchial
26	chr11:66004000-66020800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:66006800-66024600	Weak transcription	Ovary	ovary
28	chr11:66007000-66024200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:66007200-66024200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:66007800-66024200	Weak transcription	Small Intestine	intestine
31	chr11:66008000-66023800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:66008200-66021200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:66009200-66024000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:66009600-66023600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:66009800-66023000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:66009800-66024000	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:66010400-66024200	Weak transcription	Stomach Mucosa	stomach
38	chr11:66010600-66024000	Weak transcription	Primary B cells from cord blood	blood
39	chr11:66010600-66024200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:66010600-66024200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:66010600-66024600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:66010800-66024000	Weak transcription	Dnd41	blood
43	chr11:66010800-66024200	Weak transcription	Colonic Mucosa	Colon
44	chr11:66011000-66024400	Weak transcription	Right Atrium	heart
45	chr11:66011200-66020800	Weak transcription	Fetal Brain Male	brain
46	chr11:66011400-66019000	Strong transcription	Fetal Stomach	stomach
47	chr11:66011800-66024200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:66011800-66024400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:66012200-66018400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr11:66012200-66018600	Strong transcription	Fetal Muscle Leg	muscle

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