Variant report

Variant	rs12138024
Chromosome Location	chr1:112936760-112936761
allele	A/G
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	FOS	chr1:112936689-112937612	MCF10A-Er-Src	breast:	n/a	chr1:112936892-112936902 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
2	SPI1	chr1:112936741-112937290	HL-60	blood:	n/a	chr1:112936959-112936968 chr1:112936957-112936970 chr1:112936958-112936971
3	GTF3C2	chr1:112936263-112937447	Hela-S3	cervix:	n/a	n/a
4	ZNF384	chr1:112936630-112937433	K562	blood:	n/a	n/a
5	FOSL2	chr1:112936547-112937599	SK-N-SH	brain:	n/a	chr1:112936892-112936902 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
6	ZNF384	chr1:112936443-112937357	GM12878	blood:	n/a	n/a
7	ELF1	chr1:112936695-112937219	SK-N-SH	brain:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
8	POLR2A	chr1:112936682-112937454	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr1:112936297-112937581	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
11	SPI1	chr1:112936583-112937420	GM12878	blood:	n/a	chr1:112936959-112936968 chr1:112936957-112936970 chr1:112936958-112936971
12	ELF1	chr1:112936730-112937200	MCF-7	breast:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
13	SMC3	chr1:112936202-112937543	Hela-S3	cervix:	n/a	n/a
14	EP300	chr1:112936685-112937553	Hela-S3	cervix:	n/a	chr1:112937331-112937341
15	POLR2A	chr1:112936666-112937267	SK-N-SH	brain:	n/a	n/a
16	CEBPB	chr1:112936431-112937415	HCT-116	colon:	n/a	n/a
17	STAT3	chr1:112936753-112937669	MCF10A-Er-Src	breast:	n/a	chr1:112937426-112937437
18	YY1	chr1:112936709-112937342	SK-N-SH	brain:	n/a	n/a
19	PBX3	chr1:112936741-112937292	SK-N-SH	brain:	n/a	n/a
20	JUN	chr1:112936350-112937797	Hela-S3	cervix:	n/a	chr1:112936892-112936902 chr1:112937665-112937676 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
21	ELF1	chr1:112936683-112937235	GM12878	blood:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
22	IKZF1	chr1:112936708-112937525	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:112936327-112939968	Hela-S3	cervix:	n/a	n/a
24	MYC	chr1:112936712-112937534	MCF10A-Er-Src	breast:	n/a	n/a
25	TEAD4	chr1:112936712-112937494	K562	blood:	n/a	n/a
26	CEBPB	chr1:112936545-112937128	A549	lung:	n/a	n/a
27	TAF1	chr1:112936671-112937469	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr1:112936748-112937799	IMR90	lung:	n/a	n/a
29	FOS	chr1:112936339-112937769	MCF10A-Er-Src	breast:	n/a	chr1:112936892-112936902 chr1:112937665-112937676 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
30	RAD21	chr1:112936668-112937689	SK-N-SH	brain:	n/a	n/a
31	FOSL2	chr1:112936644-112937201	A549	lung:	n/a	chr1:112936892-112936902 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
32	TCF12	chr1:112936672-112937336	SK-N-SH	brain:	n/a	n/a
33	FOS	chr1:112936758-112937096	Hela-S3	cervix:	n/a	chr1:112936892-112936902 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901
34	ATF2	chr1:112936687-112937228	GM12878	blood:	n/a	n/a
35	CEBPB	chr1:112936660-112936998	ECC-1	luminal epithelium:	n/a	n/a
36	RCOR1	chr1:112936757-112937623	K562	blood:	n/a	n/a
37	ATF2	chr1:112936736-112937118	GM12878	blood:	n/a	n/a
38	CEBPB	chr1:112936632-112937490	A549	lung:	n/a	n/a
39	IRF4	chr1:112936678-112937133	GM12878	blood:	n/a	n/a
40	CEBPB	chr1:112936664-112936886	K562	blood:	n/a	n/a
41	SPI1	chr1:112936728-112937094	GM12878	blood:	n/a	chr1:112936959-112936968 chr1:112936957-112936970 chr1:112936958-112936971
42	SPI1	chr1:112936750-112937186	HL-60	blood:	n/a	chr1:112936959-112936968 chr1:112936957-112936970 chr1:112936958-112936971
43	POLR2A	chr1:112936670-112937230	GM12892	blood:	n/a	n/a
44	GATA2	chr1:112936760-112938004	HUVEC	blood vessel:	n/a	chr1:112937000-112937010 chr1:112936891-112936900
45	FOXM1	chr1:112936617-112937392	GM12878	blood:	n/a	n/a
46	YY1	chr1:112936756-112937026	HCT-116	colon:	n/a	n/a
47	REST	chr1:112936671-112937183	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr1:112936667-112938337	U87	brain:	n/a	n/a
49	POLR2A	chr1:112935643-112940520	HUVEC	blood vessel:	n/a	n/a
50	CHD2	chr1:112936757-112937488	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:112936058..112938767-chr1:113217023..113219296,3	MCF-7	breast:
3	chr1:112936014..112938715-chr1:113162685..113165273,2	K562	blood:
4	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
5	chr1:112935217..112937989-chr1:113105345..113107131,2	K562	blood:
6	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
7	chr1:112935506..112938750-chr1:113247926..113251541,4	MCF-7	breast:
8	chr1:112934882..112937734-chr1:113160574..113162558,3	K562	blood:
9	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
10	chr1:112934954..112937732-chr1:113156801..113159593,3	MCF-7	breast:
11	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
12	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
13	chr1:112935857..112936857-chr1:113008833..113009341,2	MCF-7	breast:
14	chr1:112934517..112936780-chr1:113213941..113216268,2	MCF-7	breast:
15	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
16	chr1:112936501..112937762-chr1:113156864..113157564,3	K562	blood:

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000155366	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11102471	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12080074	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1419041	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891705	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488762	0.90[ASN][1000 genomes]
rs2488763	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488765	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488768	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488769	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488770	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492501	0.87[ASN][1000 genomes]
rs2492502	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492503	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492504	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999472	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240532	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415832	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12138024	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112934000-112937200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:112934000-112937200	Weak transcription	Liver	Liver
3	chr1:112934000-112937600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:112934000-112938000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:112934000-112938000	Weak transcription	Pancreas	Pancrea
6	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:112934200-112936800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:112934200-112936800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:112934200-112937000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:112934200-112937000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:112934200-112937000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:112934200-112937000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:112934200-112937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:112934200-112937000	Weak transcription	Brain Anterior Caudate	brain
15	chr1:112934200-112937000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:112934200-112937000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:112934200-112937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:112934200-112937200	Weak transcription	Ovary	ovary
19	chr1:112934200-112937200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:112934200-112937200	Weak transcription	Spleen	Spleen
21	chr1:112934200-112937600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:112934200-112937600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:112934200-112937600	Weak transcription	Esophagus	oesophagus
24	chr1:112934200-112937600	Weak transcription	Right Ventricle	heart
25	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:112934200-112938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:112934200-112938000	Weak transcription	Gastric	stomach
28	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:112934400-112936800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:112934400-112937000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:112934400-112937000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:112934400-112937000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:112934400-112937000	Weak transcription	Brain Substantia Nigra	brain
34	chr1:112934400-112937000	Enhancers	NHEK	skin
35	chr1:112934400-112937200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:112934400-112937200	Weak transcription	Fetal Brain Male	brain
37	chr1:112934400-112937200	Weak transcription	Fetal Heart	heart
38	chr1:112934400-112937200	Weak transcription	Fetal Lung	lung
39	chr1:112934400-112937200	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:112934400-112937200	Weak transcription	Fetal Stomach	stomach
41	chr1:112934400-112937200	Weak transcription	Lung	lung
42	chr1:112934400-112937200	Weak transcription	Psoas Muscle	Psoas
43	chr1:112934400-112937200	Weak transcription	Dnd41	blood
44	chr1:112934400-112938000	Enhancers	Colon Smooth Muscle	Colon
45	chr1:112934400-112938200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:112934600-112937400	Weak transcription	Fetal Brain Female	brain
47	chr1:112934600-112937600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:112934600-112938200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:112934800-112937000	Enhancers	HMEC	breast
50	chr1:112934800-112938600	Flanking Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links