Variant report

Variant	rs16933823
Chromosome Location	chr11:17099613-17099614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:433)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:433 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr11:17098740-17100154	GM12891	blood:	n/a	n/a
2	MAX	chr11:17098969-17100077	A549	lung:	n/a	chr11:17099128-17099138
3	POU2F2	chr11:17098883-17100143	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:17097787-17100225	GM12891	blood:	n/a	n/a
5	YY1	chr11:17098138-17100190	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr11:17098062-17100249	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:17098648-17100585	K562	blood:	n/a	n/a
8	USF2	chr11:17099364-17099696	K562	blood:	n/a	n/a
9	TEAD4	chr11:17098947-17099923	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr11:17093708-17100104	MCF10A-Er-Src	breast:	n/a	n/a
11	MXI1	chr11:17098341-17099796	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr11:17099023-17099646	HepG2	liver:	n/a	chr11:17099558-17099568 chr11:17099103-17099116
13	GTF2B	chr11:17098933-17099745	K562	blood:	n/a	n/a
14	BCLAF1	chr11:17098617-17099993	GM12878	blood:	n/a	chr11:17099254-17099263 chr11:17099676-17099689 chr11:17099091-17099104
15	MAZ	chr11:17099029-17099677	GM12878	blood:	n/a	chr11:17099128-17099138
16	YY1	chr11:17099007-17099703	NT2-D1	testis:	n/a	n/a
17	SP1	chr11:17098813-17100011	A549	lung:	n/a	chr11:17099121-17099135 chr11:17098936-17098945 chr11:17099293-17099305 chr11:17099293-17099304 chr11:17099290-17099304 chr11:17099128-17099137 chr11:17099129-17099138 chr11:17099127-17099139
18	USF2	chr11:17099172-17099815	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr11:17099029-17099993	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr11:17098653-17099649	ECC-1	luminal epithelium:	n/a	n/a
21	MXI1	chr11:17098545-17100151	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:17098877-17099740	A549	lung:	n/a	n/a
23	UBTF	chr11:17098948-17100483	K562	blood:	n/a	n/a
24	YY1	chr11:17098617-17100362	H1-hESC	embryonic stem cell:	n/a	n/a
25	RCOR1	chr11:17099047-17099686	Hela-S3	cervix:	n/a	n/a
26	CHD1	chr11:17098364-17100108	GM12878	blood:	n/a	n/a
27	MYC	chr11:17099002-17099716	MCF10A-Er-Src	breast:	n/a	chr11:17099128-17099138
28	MYC	chr11:17098216-17099996	K562	blood:	n/a	chr11:17099128-17099138
29	POLR2A	chr11:17093738-17102258	K562	blood:	n/a	n/a
30	YY1	chr11:17098573-17100218	GM12878	blood:	n/a	n/a
31	RUNX3	chr11:17098463-17100087	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:17098071-17099662	HepG2	liver:	n/a	n/a
33	MAX	chr11:17098206-17100251	A549	lung:	n/a	chr11:17099128-17099138
34	E2F4	chr11:17099005-17099826	K562	blood:	n/a	chr11:17099491-17099500 chr11:17099427-17099438
35	POLR2A	chr11:17098979-17099700	HepG2	liver:	n/a	n/a
36	TAF1	chr11:17098850-17100359	H1-hESC	embryonic stem cell:	n/a	n/a
37	GABPA	chr11:17098814-17099695	K562	blood:	n/a	n/a
38	POLR2A	chr11:17098821-17099942	A549	lung:	n/a	n/a
39	ELF1	chr11:17098999-17099750	MCF-7	breast:	n/a	chr11:17099250-17099263
40	MBD4	chr11:17098942-17099712	HepG2	liver:	n/a	n/a
41	MAX	chr11:17098884-17099909	MCF-7	breast:	n/a	chr11:17099128-17099138
42	FOXA2	chr11:17099072-17099745	A549	lung:	n/a	n/a
43	ZKSCAN1	chr11:17098966-17099676	Hela-S3	cervix:	n/a	n/a
44	KAP1	chr11:17098920-17099702	U2OS	brain:	n/a	n/a
45	FOSL2	chr11:17098848-17100047	A549	lung:	n/a	n/a
46	POLR2A	chr11:17098256-17099980	PANC-1	pancreas:	n/a	n/a
47	BRCA1	chr11:17098907-17099643	Hela-S3	cervix:	n/a	n/a
48	TCF7L2	chr11:17098999-17099902	HCT-116	colon:	n/a	n/a
49	ZMIZ1	chr11:17098985-17099951	K562	blood:	n/a	n/a
50	POLR2A	chr11:17094321-17099956	PFSK-1	brain:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17098735..17099667-chr14:58764100..58764851,2	Hela-S3	cervix:
2	chr11:16804738..16808801-chr11:17097608..17100627,5	K562	blood:
3	chr11:16759714..16761562-chr11:17097936..17099803,2	K562	blood:
4	chr11:17099374..17099910-chr8:101252948..101253448,2	Hela-S3	cervix:
5	chr11:17099350..17101330-chr11:17109097..17111339,2	K562	blood:
6	chr11:16759714..16762827-chr11:17097720..17101099,4	K562	blood:
7	chr11:17097827..17101102-chr11:17296839..17299555,4	K562	blood:
8	chr11:17097769..17100478-chr3:143690055..143692307,2	MCF-7	breast:
9	chr11:17097070..17101102-chr11:17296326..17299484,3	K562	blood:
10	chr11:17027622..17030583-chr11:17098379..17100590,2	K562	blood:
11	chr11:16759176..16761906-chr11:17098692..17100616,2	MCF-7	breast:
12	chr11:17034631..17037564-chr11:17097951..17099758,2	MCF-7	breast:
13	chr1:145382425..145382977-chr11:17099070..17099873,2	Hela-S3	cervix:
14	chr11:17096429..17100576-chr11:17227768..17230724,6	K562	blood:
15	chr1:59250751..59251306-chr11:17098840..17099721,2	Hela-S3	cervix:
16	chr11:16960761..16963314-chr11:17099363..17101117,2	MCF-7	breast:
17	chr11:17099021..17099705-chr8:144853715..144854564,2	HCT-116	colon:
18	chr11:17099259..17099916-chr12:109251092..109252049,2	Hela-S3	cervix:
19	chr11:17097208..17101887-chr11:17227768..17230798,9	K562	blood:
20	chr11:17098478..17100931-chr17:59476241..59478619,2	MCF-7	breast:
21	chr11:17097048..17102595-chr11:17228016..17231208,7	MCF-7	breast:
22	chr11:17008798..17010671-chr11:17099542..17102207,2	MCF-7	breast:
23	chr11:17099367..17099933-chr6:25962975..25963522,2	NB4	blood:
24	chr11:17099359..17101768-chr11:17550989..17553473,2	K562	blood:
25	chr11:17098909..17099895-chr11:67777395..67778002,2	Hela-S3	cervix:
26	chr11:17098925..17099839-chr5:32312636..32313374,2	Hela-S3	cervix:
27	chr11:17099339..17100906-chr17:80692924..80694500,2	MCF-7	breast:
28	chr11:17097742..17101154-chr11:17227974..17231312,6	MCF-7	breast:

No data

Variant related genes	Relation type
SNORD14B	TF binding region
RPS13	TF binding region
SNORD14A	TF binding region
ENSG00000166689	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000184669	Chromatin interaction
ENSG00000110696	Chromatin interaction
ENSG00000254973	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000011405	Chromatin interaction
ENSG00000070081	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000266493	Chromatin interaction
ENSG00000167363	Chromatin interaction
ENSG00000084112	Chromatin interaction
ENSG00000257621	Chromatin interaction
ENSG00000006534	Chromatin interaction
ENSG00000234807	Chromatin interaction
ENSG00000112343	Chromatin interaction
ENSG00000110693	Chromatin interaction
ENSG00000181744	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000150712	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11024180	0.82[ASN][1000 genomes]
rs11600230	1.00[ASN][1000 genomes]
rs11603765	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs11604470	1.00[CHB][hapmap]
rs11604561	1.00[CHB][hapmap]
rs11605718	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607974	1.00[CHB][hapmap]
rs11826970	0.82[ASN][1000 genomes]
rs12419179	1.00[ASN][1000 genomes]
rs1471980	1.00[ASN][1000 genomes]
rs16924899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933827	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933873	1.00[ASN][1000 genomes]
rs17647408	1.00[CHB][hapmap]
rs1967077	1.00[ASN][1000 genomes]
rs1974527	1.00[ASN][1000 genomes]
rs1979602	1.00[CHB][hapmap]
rs2040859	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28845191	1.00[ASN][1000 genomes]
rs35493302	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57726107	1.00[ASN][1000 genomes]
rs59545597	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60698184	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61879689	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61879695	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61879701	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16933823	MYOD1	cis	parietal	SCAN
rs16933823	NUCB2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17097200-17100000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:17097200-17100400	Active TSS	Right Ventricle	heart
3	chr11:17097600-17100600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:17097800-17100200	Active TSS	NHDF-Ad	bronchial
5	chr11:17097800-17100400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr11:17097800-17100400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:17097800-17100400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr11:17097800-17100600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:17098000-17100000	Active TSS	Ovary	ovary
10	chr11:17098200-17100000	ZNF genes & repeats	Fetal Brain Male	brain
11	chr11:17098200-17100200	Active TSS	Fetal Kidney	kidney
12	chr11:17098200-17100200	Active TSS	HSMMtube	muscle
13	chr11:17098200-17100400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:17098400-17099800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:17098400-17099800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:17098400-17099800	Active TSS	Fetal Muscle Trunk	muscle
17	chr11:17098400-17099800	Active TSS	Pancreas	Pancrea
18	chr11:17098400-17100000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:17098400-17100000	Active TSS	Aorta	Aorta
20	chr11:17098400-17100200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr11:17098400-17100200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:17098400-17100200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:17098400-17100200	Active TSS	Left Ventricle	heart
24	chr11:17098400-17100200	Active TSS	Psoas Muscle	Psoas
25	chr11:17098400-17100200	Active TSS	Rectal Smooth Muscle	rectum
26	chr11:17098400-17100200	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr11:17098400-17100200	Active TSS	Small Intestine	intestine
28	chr11:17098400-17100400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:17098400-17100400	Active TSS	Esophagus	oesophagus
30	chr11:17098400-17100600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr11:17098400-17100600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:17098400-17100600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:17098400-17100800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr11:17098600-17099800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:17098600-17099800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:17098600-17099800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:17098600-17099800	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr11:17098600-17099800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:17098600-17099800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:17098600-17099800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr11:17098600-17099800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:17098600-17099800	Active TSS	Brain Substantia Nigra	brain
43	chr11:17098600-17099800	Active TSS	Thymus	Thymus
44	chr11:17098600-17100000	Active TSS	Brain Cingulate Gyrus	brain
45	chr11:17098600-17100000	Active TSS	Duodenum Mucosa	Duodenum
46	chr11:17098600-17100000	Active TSS	Fetal Heart	heart
47	chr11:17098600-17100000	Active TSS	Fetal Thymus	thymus
48	chr11:17098600-17100000	Active TSS	Stomach Mucosa	stomach
49	chr11:17098600-17100200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr11:17098600-17100200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links