Variant report

Variant	rs2492504
Chromosome Location	chr1:112937090-112937091
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	POLR2A	chr1:112936888-112937158	ProgFib	skin:	n/a	n/a
5	ZNF384	chr1:112936630-112937433	K562	blood:	n/a	n/a
6	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
7	ZNF384	chr1:112936443-112937357	GM12878	blood:	n/a	n/a
8	ELF1	chr1:112936695-112937219	SK-N-SH	brain:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
9	FOXA2	chr1:112936988-112937481	A549	lung:	n/a	chr1:112937328-112937340
10	POLR2A	chr1:112936682-112937454	Hela-S3	cervix:	n/a	n/a
11	BRCA1	chr1:112936812-112937550	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr1:112936297-112937581	IMR90	lung:	n/a	n/a
13	CTCF	chr1:112937034-112937462	K562	blood:	n/a	n/a
14	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
15	SPI1	chr1:112936583-112937420	GM12878	blood:	n/a	chr1:112936959-112936968 chr1:112936957-112936970 chr1:112936958-112936971
16	ELF1	chr1:112936730-112937200	MCF-7	breast:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
17	CTCF	chr1:112937020-112937477	MCF-7	breast:	n/a	n/a
18	SMC3	chr1:112936202-112937543	Hela-S3	cervix:	n/a	n/a
19	BHLHE40	chr1:112936824-112937446	K562	blood:	n/a	n/a
20	BHLHE40	chr1:112936820-112937447	GM12878	blood:	n/a	n/a
21	EP300	chr1:112936685-112937553	Hela-S3	cervix:	n/a	chr1:112937331-112937341
22	POLR2A	chr1:112936666-112937267	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr1:112936431-112937415	HCT-116	colon:	n/a	n/a
24	STAT3	chr1:112936753-112937669	MCF10A-Er-Src	breast:	n/a	chr1:112937426-112937437
25	EP300	chr1:112936802-112937318	GM12878	blood:	n/a	n/a
26	REST	chr1:112936786-112937090	Hela-S3	cervix:	n/a	n/a
27	MAX	chr1:112936837-112937572	Hela-S3	cervix:	n/a	n/a
28	YY1	chr1:112936709-112937342	SK-N-SH	brain:	n/a	n/a
29	PBX3	chr1:112936741-112937292	SK-N-SH	brain:	n/a	n/a
30	FOXA1	chr1:112937082-112937451	HepG2	liver:	n/a	chr1:112937326-112937341 chr1:112937328-112937340
31	ELF1	chr1:112936786-112937122	A549	lung:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
32	RAD21	chr1:112937065-112937455	MCF-7	breast:	n/a	n/a
33	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
34	ELF1	chr1:112936786-112937298	HCT-116	colon:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
35	ELF1	chr1:112936683-112937235	GM12878	blood:	n/a	chr1:112936957-112936970 chr1:112936997-112937008
36	IKZF1	chr1:112936708-112937525	GM12878	blood:	n/a	n/a
37	RAD21	chr1:112937016-112937557	A549	lung:	n/a	n/a
38	POLR2A	chr1:112936777-112937520	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr1:112937011-112937481	A549	lung:	n/a	n/a
40	POLR2A	chr1:112936327-112939968	Hela-S3	cervix:	n/a	n/a
41	MYC	chr1:112936712-112937534	MCF10A-Er-Src	breast:	n/a	n/a
42	UBTF	chr1:112936869-112937554	K562	blood:	n/a	n/a
43	TEAD4	chr1:112936712-112937494	K562	blood:	n/a	n/a
44	SMARCC1	chr1:112936846-112939575	Hela-S3	cervix:	n/a	chr1:112936892-112936901
45	MAX	chr1:112936999-112937438	GM12878	blood:	n/a	n/a
46	CEBPB	chr1:112936545-112937128	A549	lung:	n/a	n/a
47	USF2	chr1:112936901-112937370	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:112936785-112937345	Hela-S3	cervix:	n/a	n/a
49	TAF1	chr1:112936671-112937469	Hela-S3	cervix:	n/a	n/a
50	WRNIP1	chr1:112936912-112937403	GM12878	blood:	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	chr1:112936910..112939069-chr1:113249610..113251300,2	K562	blood:
9	chr1:112934882..112937734-chr1:113160574..113162558,3	K562	blood:
10	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
11	chr1:112934954..112937732-chr1:113156801..113159593,3	MCF-7	breast:
12	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
13	chr1:112936917..112937755-chr1:113249654..113250159,2	MCF-7	breast:
14	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
15	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
16	chr1:112936863..112937935-chr1:113008492..113009571,10	MCF-7	breast:
17	chr1:112936501..112937762-chr1:113156864..113157564,3	K562	blood:

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000007341	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	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12080074	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138024	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891705	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891707	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488762	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2488765	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488770	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492501	0.87[ASN][1000 genomes]
rs2492502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999472	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240532	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415832	0.91[AMR][1000 genomes];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
rs2492504	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 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	chr1:112934200-112937200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:112934200-112937200	Weak transcription	Ovary	ovary
9	chr1:112934200-112937200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:112934200-112937200	Weak transcription	Spleen	Spleen
11	chr1:112934200-112937600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:112934200-112937600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:112934200-112937600	Weak transcription	Esophagus	oesophagus
14	chr1:112934200-112937600	Weak transcription	Right Ventricle	heart
15	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:112934200-112938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:112934200-112938000	Weak transcription	Gastric	stomach
18	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:112934400-112937200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:112934400-112937200	Weak transcription	Fetal Brain Male	brain
21	chr1:112934400-112937200	Weak transcription	Fetal Heart	heart
22	chr1:112934400-112937200	Weak transcription	Fetal Lung	lung
23	chr1:112934400-112937200	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:112934400-112937200	Weak transcription	Fetal Stomach	stomach
25	chr1:112934400-112937200	Weak transcription	Lung	lung
26	chr1:112934400-112937200	Weak transcription	Psoas Muscle	Psoas
27	chr1:112934400-112937200	Weak transcription	Dnd41	blood
28	chr1:112934400-112938000	Enhancers	Colon Smooth Muscle	Colon
29	chr1:112934400-112938200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:112934600-112937400	Weak transcription	Fetal Brain Female	brain
31	chr1:112934600-112937600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:112934600-112938200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:112934800-112938600	Flanking Active TSS	HUVEC	blood vessel
34	chr1:112936000-112938200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:112936000-112938200	Enhancers	Stomach Mucosa	stomach
36	chr1:112936000-112938400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:112936200-112937200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:112936200-112937200	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:112936200-112938000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr1:112936200-112938000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:112936200-112938200	Enhancers	Primary B cells from peripheral blood	blood
42	chr1:112936200-112938200	Enhancers	Placenta	Placenta
43	chr1:112936200-112938400	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:112936200-112938600	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:112936400-112937200	Active TSS	Left Ventricle	heart
47	chr1:112936400-112937800	Enhancers	Small Intestine	intestine
48	chr1:112936400-112938000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:112936400-112938000	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:112936400-112938200	Enhancers	Primary B cells from cord blood	blood

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