Variant report

Variant	rs2488766
Chromosome Location	chr1:112937862-112937863
allele	A/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	TEAD4	chr1:112937805-112938299	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:112937750-112938974	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:112936327-112939968	Hela-S3	cervix:	n/a	n/a
5	SMARCC1	chr1:112936846-112939575	Hela-S3	cervix:	n/a	chr1:112936892-112936901
6	REST	chr1:112937779-112940172	H1-neurons	neurons:	n/a	chr1:112938321-112938331 chr1:112938610-112938630 chr1:112938319-112938339 chr1:112939163-112939176 chr1:112938614-112938627 chr1:112938319-112938333
7	TEAD4	chr1:112937776-112938275	H1-hESC	embryonic stem cell:	n/a	n/a
8	GATA2	chr1:112936760-112938004	HUVEC	blood vessel:	n/a	chr1:112937000-112937010 chr1:112936891-112936900
9	POLR2A	chr1:112936667-112938337	U87	brain:	n/a	n/a
10	USF2	chr1:112936858-112938466	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:112935643-112940520	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:112937800-112939142	SK-N-SH	brain:	n/a	n/a
13	SP1	chr1:112937803-112938267	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:112937861-112938117	HUVEC	blood vessel:	n/a	n/a
15	MXI1	chr1:112936037-112937919	IMR90	lung:	n/a	n/a
16	TBP	chr1:112936707-112937975	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:112936686-112937990	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr1:112937747-112939748	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:112937648-112938131	ProgFib	skin:	n/a	n/a
20	POLR2A	chr1:112936688-112939208	U87	brain:	n/a	n/a
21	POLR2A	chr1:112937857-112939279	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr1:112936160-112939208	U87	brain:	n/a	n/a
23	TEAD4	chr1:112937806-112938270	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:112936796-112939729	IMR90	lung:	n/a	n/a
25	POLR2A	chr1:112935854-112937954	HUVEC	blood vessel:	n/a	n/a
26	JUND	chr1:112936580-112939535	SK-N-SH	brain:	n/a	chr1:112936892-112936902 chr1:112937665-112937676 chr1:112936892-112936902 chr1:112936891-112936903 chr1:112936892-112936902 chr1:112936893-112936901

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	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
4	chr1:112936058..112938767-chr1:113217023..113219296,3	MCF-7	breast:
5	chr1:112936014..112938715-chr1:113162685..113165273,2	K562	blood:
6	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
7	chr1:112935217..112937989-chr1:113105345..113107131,2	K562	blood:
8	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
9	chr1:112935506..112938750-chr1:113247926..113251541,4	MCF-7	breast:
10	chr1:112936910..112939069-chr1:113249610..113251300,2	K562	blood:
11	chr1:112934468..112938679-chr1:113215370..113218926,7	MCF-7	breast:
12	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
13	chr1:112937187..112939558-chr17:38473517..38475542,2	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:

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000155366	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000171492	Chromatin interaction
ENSG00000272931	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000131759	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	0.82[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];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.92[AMR][1000 genomes];0.89[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]
rs2488768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.99[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]
rs2492504	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];0.99[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
rs2488766	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112934000-112938000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:112934000-112938000	Weak transcription	Pancreas	Pancrea
3	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:112934200-112938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:112934200-112938000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:112934200-112938000	Weak transcription	Gastric	stomach
7	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:112934400-112938000	Enhancers	Colon Smooth Muscle	Colon
9	chr1:112934400-112938200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:112934600-112938200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:112934800-112938600	Flanking Active TSS	HUVEC	blood vessel
12	chr1:112936000-112938200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:112936000-112938200	Enhancers	Stomach Mucosa	stomach
14	chr1:112936000-112938400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:112936200-112938000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:112936200-112938000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:112936200-112938200	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:112936200-112938200	Enhancers	Placenta	Placenta
19	chr1:112936200-112938400	Flanking Active TSS	GM12878-XiMat	blood
20	chr1:112936200-112938600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:112936400-112938000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:112936400-112938000	Enhancers	Primary hematopoietic stem cells	blood
24	chr1:112936400-112938200	Enhancers	Primary B cells from cord blood	blood
25	chr1:112936400-112938200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:112936600-112938200	Flanking Active TSS	HepG2	liver
27	chr1:112936800-112938000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:112936800-112938000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:112936800-112938000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:112936800-112938400	Flanking Active TSS	A549	lung
31	chr1:112936800-112938600	Flanking Active TSS	HSMMtube	muscle
32	chr1:112937000-112938000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr1:112937000-112938000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr1:112937000-112938000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr1:112937000-112938000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:112937000-112938000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:112937000-112938000	Enhancers	Brain Anterior Caudate	brain
38	chr1:112937000-112938000	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:112937000-112938000	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr1:112937000-112938200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:112937000-112938200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:112937000-112938400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:112937000-112938400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:112937000-112938400	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr1:112937000-112938400	Flanking Active TSS	NHDF-Ad	bronchial
46	chr1:112937000-112938600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:112937000-112938600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:112937000-112938600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:112937000-112938600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:112937000-112938600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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