Variant report

Variant	rs6416020
Chromosome Location	chr11:18617184-18617185
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr11:18616992-18617364	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr11:18616815-18617553	IMR90	lung:	n/a	chr11:18616994-18617003
3	POLR2A	chr11:18617127-18617260	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr11:18617018-18617264	MCF-7	breast:	n/a	n/a
5	STAT3	chr11:18617091-18617185	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr11:18617000-18617348	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr11:18616949-18617212	K562	blood:	n/a	n/a
8	GTF2F1	chr11:18616999-18617369	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr11:18617088-18617305	Hela-S3	cervix:	n/a	n/a
10	FOS	chr11:18617000-18617336	MCF10A-Er-Src	breast:	n/a	n/a
11	SIN3AK20	chr11:18616867-18617456	MCF-7	breast:	n/a	n/a
12	MXI1	chr11:18616715-18617435	SK-N-SH	brain:	n/a	chr11:18616994-18617003
13	FOS	chr11:18617013-18617312	MCF10A-Er-Src	breast:	n/a	n/a
14	RCOR1	chr11:18616383-18617743	IMR90	lung:	n/a	n/a
15	MYC	chr11:18616933-18617446	MCF10A-Er-Src	breast:	n/a	n/a
16	MAX	chr11:18616933-18617439	MCF-7	breast:	n/a	n/a
17	CEBPB	chr11:18616924-18617324	IMR90	lung:	n/a	n/a
18	FOS	chr11:18616991-18617312	MCF10A-Er-Src	breast:	n/a	n/a
19	MAFK	chr11:18616913-18617281	IMR90	lung:	n/a	n/a
20	MAX	chr11:18616997-18617356	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr11:18617027-18617239	Hela-S3	cervix:	n/a	n/a
22	MYC	chr11:18617120-18617213	MCF-7	breast:	n/a	n/a
23	MAX	chr11:18617030-18617325	SK-N-SH	brain:	n/a	n/a
24	USF2	chr11:18617077-18617343	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18608159..18612115-chr11:18615596..18618860,5	MCF-7	breast:
2	chr11:18615620..18618161-chr11:18620162..18622897,2	K562	blood:
3	chr11:18616692..18618721-chr11:18623253..18625857,2	MCF-7	breast:
4	chr11:18608525..18612049-chr11:18615119..18618882,10	MCF-7	breast:
5	chr11:18616067..18617811-chr11:18630289..18631863,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UEVLD-3	chr11:18617006-18617196	NONHSAT018301

No data

Variant related genes	Relation type
SPTY2D1-AS1	TF binding region
ENSG00000151116	Chromatin interaction
ENSG00000247595	Chromatin interaction
ENSG00000256282	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10500835	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11024677	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11024688	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs11024715	1.00[JPT][hapmap]
rs11024725	0.80[ASN][1000 genomes]
rs11024726	0.80[ASN][1000 genomes]
rs11024727	0.81[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024728	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12222154	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs12289223	0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs12421394	1.00[JPT][hapmap]
rs16935541	1.00[JPT][hapmap]
rs16935559	1.00[JPT][hapmap]
rs16935575	1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs1979051	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983124	0.94[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2121387	0.94[CEU][hapmap];0.82[ASN][1000 genomes]
rs2279902	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2292179	1.00[JPT][hapmap]
rs3781640	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4436523	0.81[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55969503	0.80[ASN][1000 genomes]
rs7105387	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72881309	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	esv2761651	chr11:18606832-18621409	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6416020	UEVLD	cis	cerebellum	SCAN
rs6416020	NUCB2	cis	cerebellum	SCAN
rs6416020	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs6416020	TSG101	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18611000-18628600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:18611200-18628600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:18611200-18636400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:18611400-18627600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:18611400-18635800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:18611600-18617200	Weak transcription	Fetal Intestine Small	intestine
7	chr11:18611600-18617200	Weak transcription	Fetal Lung	lung
8	chr11:18611600-18627200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:18611600-18627200	Weak transcription	Brain Germinal Matrix	brain
10	chr11:18611600-18629200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:18611600-18629600	Weak transcription	Fetal Kidney	kidney
12	chr11:18611800-18617400	Weak transcription	Right Ventricle	heart
13	chr11:18611800-18621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:18611800-18627200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:18611800-18636200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:18612000-18617200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:18612000-18617200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:18612000-18617200	Weak transcription	Aorta	Aorta
19	chr11:18612000-18629600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:18612000-18630800	Weak transcription	Colonic Mucosa	Colon
21	chr11:18612000-18636200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:18612200-18617200	Weak transcription	Fetal Brain Female	brain
23	chr11:18612200-18617200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:18612200-18629800	Weak transcription	HUVEC	blood vessel
25	chr11:18612400-18617200	Weak transcription	NHLF	lung
26	chr11:18612400-18617400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr11:18612400-18627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:18612400-18631000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:18612400-18638400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:18612600-18617200	Weak transcription	Liver	Liver
31	chr11:18612600-18617200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:18612600-18617200	Weak transcription	Spleen	Spleen
33	chr11:18612800-18617200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:18612800-18617200	Weak transcription	Brain Substantia Nigra	brain
35	chr11:18612800-18617200	Weak transcription	HSMM	muscle
36	chr11:18612800-18617200	Weak transcription	Osteobl	bone
37	chr11:18612800-18617400	Weak transcription	Gastric	stomach
38	chr11:18612800-18628800	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:18612800-18629600	Weak transcription	Stomach Mucosa	stomach
40	chr11:18612800-18630800	Weak transcription	HSMMtube	muscle
41	chr11:18613000-18617200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr11:18613000-18617400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:18613000-18619200	Weak transcription	Fetal Heart	heart
44	chr11:18613000-18628800	Weak transcription	K562	blood
45	chr11:18613400-18617400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:18613800-18617200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:18614200-18627400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:18614600-18631000	Weak transcription	HepG2	liver
49	chr11:18615400-18617200	Enhancers	Placenta	Placenta
50	chr11:18615600-18617200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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