Variant report

Variant	rs2488765
Chromosome Location	chr1:112938917-112938918
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	POLR2A	chr1:112938334-112939103	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr1:112938415-112939062	K562	blood:	n/a	n/a
3	POLR2A	chr1:112938754-112938996	HepG2	liver:	n/a	n/a
4	TAF1	chr1:112938446-112939165	H1-neurons	neurons:	n/a	n/a
5	GABPA	chr1:112938309-112939044	SK-N-SH	brain:	n/a	chr1:112939019-112939028
6	CREB1	chr1:112938237-112939088	HepG2	liver:	n/a	n/a
7	MAX	chr1:112938389-112939002	A549	lung:	n/a	n/a
8	POLR2A	chr1:112938385-112939125	HCT-116	colon:	n/a	n/a
9	NFYA	chr1:112938091-112939177	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr1:112938450-112939002	HepG2	liver:	n/a	n/a
11	SP1	chr1:112938419-112939054	H1-hESC	embryonic stem cell:	n/a	chr1:112939020-112939029 chr1:112938726-112938738 chr1:112938821-112938833 chr1:112939019-112939029 chr1:112939020-112939029 chr1:112939018-112939030 chr1:112938727-112938736 chr1:112938821-112938833 chr1:112939018-112939030 chr1:112938728-112938737 chr1:112939019-112939029 chr1:112938818-112938832 chr1:112938822-112938831 chr1:112938727-112938741 chr1:112938823-112938832 chr1:112938726-112938737 chr1:112939019-112939028 chr1:112939015-112939029
12	RCOR1	chr1:112937996-112939603	Hela-S3	cervix:	n/a	n/a
13	NFYA	chr1:112938285-112939153	K562	blood:	n/a	n/a
14	POLR2A	chr1:112938449-112939121	Gliobla	brain:	n/a	n/a
15	CHD2	chr1:112938431-112939603	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:112938338-112939881	H1-neurons	neurons:	n/a	n/a
17	SP1	chr1:112938406-112939115	H1-hESC	embryonic stem cell:	n/a	chr1:112939020-112939029 chr1:112938726-112938738 chr1:112938821-112938833 chr1:112939019-112939029 chr1:112939020-112939029 chr1:112939018-112939030 chr1:112938727-112938736 chr1:112938821-112938833 chr1:112939018-112939030 chr1:112938728-112938737 chr1:112939019-112939029 chr1:112938818-112938832 chr1:112938822-112938831 chr1:112938727-112938741 chr1:112938823-112938832 chr1:112938726-112938737 chr1:112939019-112939028 chr1:112939015-112939029
18	POLR2A	chr1:112938736-112939255	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:112938371-112939167	ECC-1	luminal epithelium:	n/a	n/a
21	MAZ	chr1:112938328-112939554	K562	blood:	n/a	chr1:112939017-112939027
22	POLR2A	chr1:112938387-112940060	GM19099	blood:	n/a	n/a
23	ZNF143	chr1:112938457-112939264	H1-hESC	embryonic stem cell:	n/a	chr1:112939035-112939053
24	POLR2A	chr1:112938419-112939103	A549	lung:	n/a	n/a
25	HMGN3	chr1:112938484-112939065	K562	blood:	n/a	n/a
26	CHD2	chr1:112938483-112938993	H1-hESC	embryonic stem cell:	n/a	n/a
27	PBX3	chr1:112938500-112939103	A549	lung:	n/a	chr1:112938782-112938802
28	GABPA	chr1:112938308-112939028	MCF-7	breast:	n/a	chr1:112939019-112939028
29	FOS	chr1:112938583-112938962	K562	blood:	n/a	n/a
30	SIN3A	chr1:112938526-112939030	GM12878	blood:	n/a	chr1:112938814-112938825
31	IRF3	chr1:112938606-112938952	Hela-S3	cervix:	n/a	chr1:112938724-112938738 chr1:112938821-112938835
32	MAX	chr1:112938436-112939776	GM12878	blood:	n/a	chr1:112939017-112939027
33	EP300	chr1:112938908-112939091	GM12878	blood:	n/a	n/a
34	PBX3	chr1:112938546-112938977	A549	lung:	n/a	chr1:112938782-112938802
35	REST	chr1:112938309-112939738	H1-neurons	neurons:	n/a	chr1:112938321-112938331 chr1:112938610-112938630 chr1:112938319-112938339 chr1:112939163-112939176 chr1:112938614-112938627 chr1:112938319-112938333
36	POLR2A	chr1:112938377-112939198	U87	brain:	n/a	n/a
37	SP2	chr1:112938568-112938963	HepG2	liver:	n/a	chr1:112938779-112938802 chr1:112938726-112938741
38	E2F4	chr1:112938577-112938919	MCF10A-Er-Src	breast:	n/a	chr1:112938728-112938737 chr1:112938739-112938748
39	GTF2F1	chr1:112938497-112939085	Hela-S3	cervix:	n/a	n/a
40	CREB1	chr1:112938338-112939047	HepG2	liver:	n/a	n/a
41	SP4	chr1:112938551-112939098	H1-hESC	embryonic stem cell:	n/a	chr1:112939016-112939032 chr1:112939014-112939030 chr1:112938817-112938833 chr1:112938724-112938740 chr1:112938726-112938737 chr1:112938819-112938835
42	POLR2A	chr1:112937750-112938974	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:112938015-112939192	HepG2	liver:	n/a	n/a
44	EBF1	chr1:112938620-112939640	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:112938286-112939077	MCF10A-Er-Src	breast:	n/a	n/a
46	JUND	chr1:112938376-112939056	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:112938311-112939149	PANC-1	pancreas:	n/a	n/a
48	CREB1	chr1:112938355-112939080	H1-hESC	embryonic stem cell:	n/a	n/a
49	ZNF143	chr1:112938470-112939096	Hela-S3	cervix:	n/a	chr1:112939035-112939053
50	SP2	chr1:112938564-112938925	H1-hESC	embryonic stem cell:	n/a	chr1:112938779-112938802 chr1:112938726-112938741

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:90285374..90287672-chr1:112937742..112939314,2	MCF-7	breast:
3	chr1:112938137..112939101-chr16:67207540..67208291,2	Hela-S3	cervix:
4	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
5	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
6	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
7	chr1:112936910..112939069-chr1:113249610..113251300,2	K562	blood:
8	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
9	chr1:112938289..112939065-chr6:26157383..26158365,2	Hela-S3	cervix:
10	chr1:112937187..112939558-chr17:38473517..38475542,2	MCF-7	breast:
11	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
12	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
13	chr1:112938761..112941761-chr1:113247568..113249753,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WNT2B-2	chr1:112938881-112941439	NONHSAT005231

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000272931	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000140939	Chromatin interaction
ENSG00000171492	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000158373	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	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12080074	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138024	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1419041	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488762	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2488763	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2488766	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488768	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488769	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488770	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492501	0.86[ASN][1000 genomes]
rs2492502	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492503	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492504	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999472	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240532	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415832	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[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
rs2488765	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:112937000-112940000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:112938000-112940000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:112938000-112940000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:112938000-112940000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:112938000-112941000	Active TSS	Aorta	Aorta
7	chr1:112938200-112939000	Active TSS	HepG2	liver
8	chr1:112938200-112939400	Active TSS	Colon Smooth Muscle	Colon
9	chr1:112938200-112939600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
10	chr1:112938200-112939600	Active TSS	Fetal Brain Female	brain
11	chr1:112938200-112939600	Active TSS	Placenta Amnion	Placenta Amnion
12	chr1:112938200-112939800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:112938200-112939800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:112938200-112939800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:112938200-112939800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:112938200-112939800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:112938200-112939800	Active TSS	Ovary	ovary
18	chr1:112938200-112939800	Active TSS	Psoas Muscle	Psoas
19	chr1:112938200-112939800	Active TSS	Spleen	Spleen
20	chr1:112938200-112940000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:112938200-112940000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:112938200-112940000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:112938200-112940000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:112938200-112940000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr1:112938200-112940000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:112938200-112940200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:112938200-112940200	Active TSS	Right Ventricle	heart
28	chr1:112938200-112940400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:112938200-112940400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:112938200-112940400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:112938200-112941200	Active TSS	Right Atrium	heart
32	chr1:112938200-112941400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:112938400-112939200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:112938400-112939200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:112938400-112939200	Active TSS	Colonic Mucosa	Colon
36	chr1:112938400-112939200	Active TSS	Fetal Muscle Trunk	muscle
37	chr1:112938400-112939200	Active TSS	Fetal Thymus	thymus
38	chr1:112938400-112939200	Active TSS	Thymus	Thymus
39	chr1:112938400-112939400	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr1:112938400-112939400	Active TSS	Brain Angular Gyrus	brain
41	chr1:112938400-112939400	Active TSS	Brain Hippocampus Middle	brain
42	chr1:112938400-112939400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:112938400-112939400	Active TSS	Fetal Lung	lung
44	chr1:112938400-112939400	Active TSS	Fetal Muscle Leg	muscle
45	chr1:112938400-112939400	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:112938400-112939600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:112938400-112939600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:112938400-112939600	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:112938400-112939600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:112938400-112939600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood

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