Variant report

Variant	rs2658554
Chromosome Location	chr11:18512966-18512967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TRIM28	chr11:18512529-18513093	K562	blood:	n/a	n/a
2	STAT5A	chr11:18512559-18513114	K562	blood:	n/a	n/a
3	EP300	chr11:18512659-18513034	K562	blood:	n/a	n/a
4	TBL1XR1	chr11:18512550-18513034	K562	blood:	n/a	n/a
5	POLR2A	chr11:18512728-18513017	K562	blood:	n/a	n/a
6	PML	chr11:18512572-18513075	K562	blood:	n/a	n/a
7	MYC	chr11:18512701-18513129	K562	blood:	n/a	n/a
8	JUND	chr11:18512628-18513058	K562	blood:	n/a	n/a
9	RCOR1	chr11:18512570-18513056	K562	blood:	n/a	n/a
10	ATF1	chr11:18512610-18512972	K562	blood:	n/a	n/a
11	CCNT2	chr11:18512616-18513161	K562	blood:	n/a	n/a
12	RCOR1	chr11:18512609-18513071	K562	blood:	n/a	n/a
13	POLR2A	chr11:18512739-18513024	K562	blood:	n/a	n/a
14	CEBPD	chr11:18512566-18513121	K562	blood:	n/a	n/a
15	NR2F2	chr11:18512600-18513161	K562	blood:	n/a	n/a
16	TEAD4	chr11:18512560-18513198	K562	blood:	n/a	n/a
17	REST	chr11:18512735-18512977	K562	blood:	n/a	n/a
18	CEBPD	chr11:18512584-18513091	K562	blood:	n/a	n/a
19	MAX	chr11:18512966-18513179	K562	blood:	n/a	n/a
20	HDAC2	chr11:18512657-18513034	K562	blood:	n/a	n/a
21	MAZ	chr11:18512700-18513002	K562	blood:	n/a	n/a
22	MYC	chr11:18512653-18513056	K562	blood:	n/a	n/a
23	ELF1	chr11:18512697-18512968	K562	blood:	n/a	n/a
24	TEAD4	chr11:18512571-18513131	K562	blood:	n/a	n/a
25	TAL1	chr11:18512636-18513076	K562	blood:	n/a	n/a
26	HMGN3	chr11:18512700-18513059	K562	blood:	n/a	n/a
27	PML	chr11:18512581-18513055	K562	blood:	n/a	n/a
28	NR2F2	chr11:18512627-18513172	K562	blood:	n/a	n/a
29	GATA1	chr11:18512518-18513604	K562	blood:	n/a	n/a
30	HDAC2	chr11:18512648-18513030	K562	blood:	n/a	n/a
31	GATA2	chr11:18512613-18513076	K562	blood:	n/a	n/a
32	POLR2A	chr11:18512583-18513021	K562	blood:	n/a	n/a
33	GABPA	chr11:18512700-18513028	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000256464	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10741745	0.84[ASN][1000 genomes]
rs10741746	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832941	0.84[ASN][1000 genomes]
rs11024694	0.88[ASN][1000 genomes]
rs11024717	0.83[CEU][hapmap];0.84[ASN][1000 genomes]
rs12361289	0.86[ASN][1000 genomes]
rs1857907	0.88[ASN][1000 genomes]
rs2132302	0.95[ASN][1000 genomes]
rs2291752	0.92[ASN][1000 genomes]
rs2643866	0.88[ASN][1000 genomes]
rs2658552	0.90[ASN][1000 genomes]
rs2658564	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2658567	0.88[ASN][1000 genomes]
rs2698567	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486430	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7119085	0.84[ASN][1000 genomes]
rs7129164	0.88[ASN][1000 genomes]
rs7940645	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	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
7	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2658554	TSG101	cis	multi-tissue	Pritchard
rs2658554	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18483600-18526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:18496000-18515200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:18496200-18513200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:18496200-18513400	Strong transcription	Fetal Muscle Leg	muscle
5	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:18497000-18513200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:18497200-18513200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:18497600-18513200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:18498800-18513600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:18499400-18513400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:18503200-18516200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:18504200-18522800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:18504600-18513000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:18504600-18523400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:18504600-18523400	Weak transcription	Small Intestine	intestine
22	chr11:18504600-18523600	Weak transcription	HMEC	breast
23	chr11:18505200-18531800	Weak transcription	Fetal Brain Male	brain
24	chr11:18506000-18519200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:18506400-18519600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:18507200-18513200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:18507400-18513200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:18507600-18516600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:18508000-18519600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:18508000-18520200	Weak transcription	Hela-S3	cervix
31	chr11:18509000-18514200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr11:18509000-18520600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:18509000-18537600	Strong transcription	Liver	Liver
34	chr11:18509000-18540200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:18509200-18513400	Strong transcription	Thymus	Thymus
37	chr11:18509200-18516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:18509200-18517600	Strong transcription	Primary T cells from cord blood	blood
39	chr11:18509400-18515800	Strong transcription	Primary B cells from cord blood	blood
40	chr11:18509400-18516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:18509600-18540200	Strong transcription	Placenta	Placenta
42	chr11:18509800-18517600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:18510000-18513200	Strong transcription	Left Ventricle	heart
44	chr11:18510200-18516800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:18510600-18513000	Strong transcription	Ovary	ovary
46	chr11:18510600-18513400	Strong transcription	Fetal Thymus	thymus
47	chr11:18510600-18513400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:18510800-18513200	Strong transcription	Fetal Brain Female	brain
49	chr11:18510800-18513400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:18510800-18513400	Genic enhancers	Brain Angular Gyrus	brain

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