Variant report

Variant	rs1419041
Chromosome Location	chr1:112938140-112938141
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYA	chr1:112938091-112939177	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr1:112937996-112939603	Hela-S3	cervix:	n/a	n/a
3	TEAD4	chr1:112937805-112938299	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:112935622-112939617	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:112937750-112938974	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:112938015-112939192	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:112936327-112939968	Hela-S3	cervix:	n/a	n/a
8	SMARCC1	chr1:112936846-112939575	Hela-S3	cervix:	n/a	chr1:112936892-112936901
9	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
10	TEAD4	chr1:112937868-112938144	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr1:112937776-112938275	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr1:112937882-112938262	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:112936667-112938337	U87	brain:	n/a	n/a
14	USF2	chr1:112936858-112938466	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:112935643-112940520	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr1:112937800-112939142	SK-N-SH	brain:	n/a	n/a
17	SP1	chr1:112937803-112938267	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:112937887-112940072	GM12878	blood:	n/a	n/a
19	TAF1	chr1:112937890-112939489	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr1:112937962-112938608	H1-hESC	embryonic stem cell:	n/a	n/a
21	MXI1	chr1:112938131-112938837	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:112937885-112938158	H1-hESC	embryonic stem cell:	n/a	n/a
23	NFYB	chr1:112938058-112939089	K562	blood:	n/a	n/a
24	ELK4	chr1:112938134-112938760	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:112937747-112939748	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:112937911-112939939	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:112936688-112939208	U87	brain:	n/a	n/a
28	POLR2A	chr1:112937857-112939279	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr1:112936160-112939208	U87	brain:	n/a	n/a
30	TEAD4	chr1:112937806-112938270	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:112936796-112939729	IMR90	lung:	n/a	n/a
32	POLR2A	chr1:112938139-112938241	ProgFib	skin:	n/a	n/a
33	POLR2A	chr1:112937919-112938284	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:112938109-112939030	MCF10A-Er-Src	breast:	n/a	n/a
35	GABPA	chr1:112938054-112939085	MCF-7	breast:	n/a	chr1:112939019-112939028
36	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 data

(count:16 , 50 per page) page: 1

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	chr1:112936058..112938767-chr1:113217023..113219296,3	MCF-7	breast:
6	chr1:112936014..112938715-chr1:113162685..113165273,2	K562	blood:
7	chr1:112936667..112940657-chr1:113004024..113011069,20	MCF-7	breast:
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	chr1:112938006..112938734-chr5:90676277..90676835,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CTTNBP2NL	TF binding region
ENSG00000007341	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000272931	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000171492	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000140939	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1018712	0.83[CEU][hapmap]
rs11102471	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1177812	0.83[CEU][hapmap]
rs12080074	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138024	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1412931	0.83[CEU][hapmap]
rs1475710	0.83[CEU][hapmap]
rs1759689	0.83[CEU][hapmap]
rs1759692	0.86[CEU][hapmap]
rs1777608	0.83[CEU][hapmap]
rs1891705	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891707	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2483328	0.83[CEU][hapmap]
rs2488758	0.83[CEU][hapmap]
rs2488762	0.92[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488763	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488765	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488766	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488769	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488770	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488787	0.83[CEU][hapmap]
rs2492501	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs2492502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492503	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492504	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492507	0.82[CEU][hapmap]
rs2492512	0.83[CEU][hapmap]
rs2492513	0.83[CEU][hapmap]
rs2492534	0.83[CEU][hapmap]
rs2999472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240532	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7415832	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7541222	0.83[CEU][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1419041	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL
rs1419041	LOC643396	cis	multi-tissue	Pritchard
rs1419041	CTTNBP2NL	cis	lymphoblastoid	seeQTL
rs1419041	CTTNBP2NL,LOC100129406	cis	brain	BrainEAC

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112934000-112938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:112934200-112938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:112934400-112938200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:112934600-112938200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:112934800-112938600	Flanking Active TSS	HUVEC	blood vessel
6	chr1:112936000-112938200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:112936000-112938200	Enhancers	Stomach Mucosa	stomach
8	chr1:112936000-112938400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:112936200-112938200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:112936200-112938200	Enhancers	Placenta	Placenta
11	chr1:112936200-112938400	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:112936200-112938600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:112936200-112940000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:112936400-112938200	Enhancers	Primary B cells from cord blood	blood
15	chr1:112936400-112938200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:112936600-112938200	Flanking Active TSS	HepG2	liver
17	chr1:112936800-112938400	Flanking Active TSS	A549	lung
18	chr1:112936800-112938600	Flanking Active TSS	HSMMtube	muscle
19	chr1:112937000-112938200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:112937000-112938200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:112937000-112938400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:112937000-112938400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:112937000-112938400	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr1:112937000-112938400	Flanking Active TSS	NHDF-Ad	bronchial
25	chr1:112937000-112938600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:112937000-112938600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:112937000-112938600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:112937000-112938600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:112937000-112938600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:112937000-112938600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr1:112937000-112938600	Flanking Active TSS	Hela-S3	cervix
32	chr1:112937000-112938600	Flanking Active TSS	NH-A	brain
33	chr1:112937000-112938600	Flanking Active TSS	NHEK	skin
34	chr1:112937000-112938600	Flanking Active TSS	NHLF	lung
35	chr1:112937000-112940000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:112937200-112938200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:112937200-112938200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:112937200-112938200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:112937200-112938200	Enhancers	Fetal Muscle Leg	muscle
40	chr1:112937200-112938200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:112937200-112938200	Enhancers	Spleen	Spleen
42	chr1:112937200-112938400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:112937200-112938400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:112937200-112938400	Enhancers	Lung	lung
45	chr1:112937200-112938400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:112937200-112938600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:112937200-112938600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:112937400-112938200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:112937400-112938200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:112937400-112938200	Enhancers	Left Ventricle	heart

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