Variant report

Variant	rs12796375
Chromosome Location	chr11:9026026-9026027
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	USF1	chr11:9025942-9026205	HepG2	liver:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
2	ATF3	chr11:9025863-9026252	H1-hESC	embryonic stem cell:	n/a	chr11:9026110-9026130 chr11:9025957-9025966
3	BACH1	chr11:9025110-9026394	H1-hESC	embryonic stem cell:	n/a	n/a
4	HMGN3	chr11:9025063-9026170	K562	blood:	n/a	chr11:9025216-9025225
5	CTCF	chr11:9025880-9026030	AG04449	skin:	n/a	chr11:9025998-9026011
6	MAX	chr11:9024938-9026279	K562	blood:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119 chr11:9026257-9026266
7	SIN3A	chr11:9025973-9026531	H1-hESC	embryonic stem cell:	n/a	chr11:9026109-9026118 chr11:9026111-9026120
8	USF1	chr11:9025904-9026290	H1-hESC	embryonic stem cell:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
9	BHLHE40	chr11:9025986-9026094	K562	blood:	n/a	n/a
10	E2F6	chr11:9025010-9026481	H1-hESC	embryonic stem cell:	n/a	chr11:9026285-9026294 chr11:9025568-9025575 chr11:9025293-9025302
11	MAZ	chr11:9024165-9026232	IMR90	lung:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119
12	USF1	chr11:9025991-9026230	K562	blood:	n/a	chr11:9026109-9026120
13	CTBP2	chr11:9025816-9026376	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr11:9025943-9026343	SK-N-SH_RA	brain:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
15	MAX	chr11:9025326-9026276	HepG2	liver:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119 chr11:9026257-9026266
16	USF2	chr11:9025911-9026304	H1-hESC	embryonic stem cell:	n/a	chr11:9025956-9025972
17	MAX	chr11:9024992-9026277	SK-N-SH	brain:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119 chr11:9026257-9026266
18	USF1	chr11:9025985-9026211	HepG2	liver:	n/a	chr11:9026109-9026120
19	USF1	chr11:9025836-9026370	H1-hESC	embryonic stem cell:	n/a	chr11:9025956-9025972 chr11:9026109-9026120 chr11:9025868-9025884
20	E2F6	chr11:9024972-9026595	H1-hESC	embryonic stem cell:	n/a	chr11:9026285-9026294 chr11:9025568-9025575 chr11:9025293-9025302
21	USF1	chr11:9025765-9026411	SK-N-SH	brain:	n/a	chr11:9025956-9025972 chr11:9026109-9026120 chr11:9025868-9025884
22	MAX	chr11:9025027-9026564	H1-hESC	embryonic stem cell:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119 chr11:9026527-9026535 chr11:9026257-9026266 chr11:9026302-9026311
23	TBP	chr11:9024942-9026175	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF1	chr11:9026013-9026204	GM12878	blood:	n/a	chr11:9026109-9026120
25	USF1	chr11:9025955-9026281	K562	blood:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
26	E2F6	chr11:9025024-9026170	K562	blood:	n/a	chr11:9025568-9025575 chr11:9025293-9025302
27	MAX	chr11:9025042-9026568	H1-hESC	embryonic stem cell:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119 chr11:9026527-9026535 chr11:9026257-9026266 chr11:9026302-9026311
28	USF1	chr11:9025903-9026281	SK-N-SH_RA	brain:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
29	USF1	chr11:9025893-9026284	SK-N-SH	brain:	n/a	chr11:9025956-9025972 chr11:9026109-9026120
30	SIN3AK20	chr11:9025041-9026103	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr11:9024936-9026060	H1-neurons	neurons:	n/a	n/a
32	MAX	chr11:9024983-9026197	HepG2	liver:	n/a	chr11:9026108-9026121 chr11:9026109-9026120 chr11:9026110-9026119 chr11:9026110-9026119
33	CTCF	chr11:9025900-9026050	SK-N-SH_RA	brain:	n/a	chr11:9025998-9026011

No.	Distal block	Cell Line	Cell type
1	chr11:8984349..8987280-chr11:9024480..9026486,3	K562	blood:
2	chr11:8713787..8716446-chr11:9025116..9027150,2	K562	blood:
3	chr11:9023701..9026254-chr11:9404770..9407613,2	K562	blood:
4	chr11:8930312..8933119-chr11:9023959..9026944,2	K562	blood:
5	chr11:8930312..8934560-chr11:9023959..9026944,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKIP1-2	chr11:9025709-9026090	ENSG00000253973.2

Variant related genes	Relation type
NRIP3	TF binding region
ENSG00000205339	Chromatin interaction
ENSG00000254665	Chromatin interaction
ENSG00000254860	Chromatin interaction
ENSG00000166444	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000175348	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1136966	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960181	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1969627	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984775	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984790	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060157	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2568078	0.81[AMR][1000 genomes]
rs2653609	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742483	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742502	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34004082	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34191466	1.00[ASN][1000 genomes]
rs35578021	1.00[ASN][1000 genomes]
rs4061640	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277831	1.00[ASN][1000 genomes]
rs7108116	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7110170	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7130454	1.00[ASN][1000 genomes]
rs71476814	1.00[ASN][1000 genomes]
rs72856032	1.00[ASN][1000 genomes]
rs7396115	1.00[ASN][1000 genomes]
rs7936201	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941341	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3354735	chr11:9024401-9026949	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12796375	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9023800-9026600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:9024400-9026200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
3	chr11:9024400-9026600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr11:9024600-9026200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:9024600-9026200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
6	chr11:9024600-9026200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:9024600-9026200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
8	chr11:9024600-9026200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr11:9024600-9026400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr11:9024600-9026400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
11	chr11:9024600-9026400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
12	chr11:9024600-9026400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:9024600-9026400	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr11:9024600-9026600	Bivalent Enhancer	Fetal Brain Male	brain
15	chr11:9024600-9027000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
17	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
18	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr11:9024800-9026200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr11:9024800-9026200	Flanking Active TSS	Ovary	ovary
23	chr11:9024800-9026200	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr11:9024800-9026400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:9024800-9026400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:9024800-9026600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:9025000-9026200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:9025000-9026200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr11:9025000-9026200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
30	chr11:9025000-9026200	Active TSS	Colon Smooth Muscle	Colon
31	chr11:9025000-9026400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:9025000-9026600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr11:9025000-9026600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr11:9025200-9026200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:9025200-9026200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:9025200-9026200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:9025200-9026200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:9025200-9026200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr11:9025200-9026200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr11:9025200-9026200	Active TSS	Rectal Smooth Muscle	rectum
41	chr11:9025200-9026400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr11:9025200-9026400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr11:9025200-9026400	Active TSS	Primary T cells from cord blood	blood
44	chr11:9025200-9026400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:9025200-9026400	Bivalent/Poised TSS	HepG2	liver
46	chr11:9025200-9026600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:9025200-9026600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:9025200-9026600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr11:9025200-9026600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:9025200-9027000	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links