Variant report

Variant	rs11659054
Chromosome Location	chr17:33867678-33867679
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	MTA3	chr17:33867539-33868305	GM12878	blood:	n/a	n/a
2	EBF1	chr17:33867549-33867986	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:33867578-33868314	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:33867473-33868330	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:33867545-33868225	HL-60	blood:	n/a	n/a
6	POLR2A	chr17:33867532-33868013	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:33867638-33867893	GM12878	blood:	n/a	n/a
8	MAX	chr17:33867638-33868073	NB4	blood:	n/a	n/a
9	TBP	chr17:33867550-33868650	GM12878	blood:	n/a	n/a
10	IRF1	chr17:33867194-33868777	K562	blood:	n/a	chr17:33868262-33868273 chr17:33868261-33868275 chr17:33868255-33868276 chr17:33868257-33868271 chr17:33868260-33868272 chr17:33868260-33868272 chr17:33868258-33868272 chr17:33868259-33868272 chr17:33868261-33868271 chr17:33868260-33868277 chr17:33868261-33868272
11	POLR2A	chr17:33867625-33867885	GM12878	blood:	n/a	n/a
12	BHLHE40	chr17:33867630-33868349	GM12878	blood:	n/a	n/a
13	SPI1	chr17:33867667-33868036	GM12891	blood:	n/a	n/a
14	EBF1	chr17:33867593-33868212	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:33867491-33868334	GM12878	blood:	n/a	n/a
16	EBF1	chr17:33867599-33867883	GM12878	blood:	n/a	n/a
17	YY1	chr17:33867593-33868195	GM12878	blood:	n/a	n/a
18	POLR2A	chr17:33867564-33868341	GM12892	blood:	n/a	n/a
19	POLR2A	chr17:33867525-33868090	HL-60	blood:	n/a	n/a
20	SPI1	chr17:33867541-33868127	HL-60	blood:	n/a	n/a
21	POLR2A	chr17:33867478-33868382	GM12878	blood:	n/a	n/a
22	REST	chr17:33867559-33868415	HL-60	blood:	n/a	n/a
23	POLR2A	chr17:33867514-33868317	GM12892	blood:	n/a	n/a
24	ZNF143	chr17:33867643-33867802	GM12878	blood:	n/a	n/a
25	MTA3	chr17:33867537-33868355	GM12878	blood:	n/a	n/a
26	YY1	chr17:33867652-33868014	GM12892	blood:	n/a	n/a
27	POLR2A	chr17:33867474-33868399	GM12892	blood:	n/a	n/a
28	MYC	chr17:33867642-33868250	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:33865333..33868494-chr17:33903936..33906030,4	K562	blood:
2	chr17:33463726..33465854-chr17:33866569..33869012,2	K562	blood:
3	chr17:33865333..33867975-chr17:33904009..33907160,3	K562	blood:
4	chr17:33865496..33867936-chr17:33913565..33917669,3	K562	blood:

Variant related genes	Relation type
SLFN12L	TF binding region
ENSG00000073536	Chromatin interaction
ENSG00000006125	Chromatin interaction
ENSG00000108733	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11080353	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080354	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080355	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150450	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17550268	0.88[ASN][1000 genomes]
rs35614987	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795082	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66878360	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7502331	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8073060	0.84[EUR][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	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574754	chr17:33841737-33881631	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11659054	LOC645744	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33862800-33869400	Weak transcription	Spleen	Spleen
2	chr17:33864200-33867800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:33864400-33867800	Weak transcription	Placenta	Placenta
4	chr17:33864400-33867800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:33864600-33867800	Weak transcription	Psoas Muscle	Psoas
6	chr17:33864600-33868000	Enhancers	Fetal Thymus	thymus
7	chr17:33864800-33867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr17:33864800-33867800	Weak transcription	Right Atrium	heart
9	chr17:33865200-33867800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:33865400-33868000	Weak transcription	Fetal Stomach	stomach
11	chr17:33866000-33867800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr17:33866000-33868000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:33866000-33869800	Enhancers	Lung	lung
14	chr17:33866400-33867800	Enhancers	HUVEC	blood vessel
15	chr17:33866400-33868000	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr17:33866400-33868000	Enhancers	Stomach Mucosa	stomach
17	chr17:33866400-33868400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr17:33866600-33867800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr17:33866600-33867800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr17:33866600-33867800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr17:33866600-33868000	Bivalent Enhancer	Fetal Lung	lung
22	chr17:33866600-33868600	Active TSS	Duodenum Mucosa	Duodenum
23	chr17:33866800-33868000	Weak transcription	Ovary	ovary
24	chr17:33866800-33868000	Enhancers	HSMM	muscle
25	chr17:33866800-33868600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:33867000-33867800	Enhancers	Primary hematopoietic stem cells	blood
27	chr17:33867000-33868000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:33867000-33868000	Weak transcription	Brain Hippocampus Middle	brain
29	chr17:33867000-33868000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr17:33867000-33868000	Enhancers	A549	lung
31	chr17:33867000-33868000	Enhancers	K562	blood
32	chr17:33867000-33868600	Enhancers	Hela-S3	cervix
33	chr17:33867200-33867800	Enhancers	Small Intestine	intestine
34	chr17:33867400-33867800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr17:33867400-33867800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr17:33867400-33867800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr17:33867400-33867800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:33867400-33867800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr17:33867400-33867800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr17:33867400-33868000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr17:33867400-33868800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr17:33867400-33868800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:33867600-33867800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:33867600-33867800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:33867600-33867800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr17:33867600-33867800	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr17:33867600-33867800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr17:33867600-33867800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr17:33867600-33867800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:33867600-33867800	Flanking Active TSS	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links