Variant report

Variant	rs2452554
Chromosome Location	chr4:95409802-95409803
allele	C/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	RAD21	chr4:95409802-95410205	IMR90	lung:	n/a	n/a
2	TBP	chr4:95409785-95410606	Hela-S3	cervix:	n/a	n/a
3	MAX	chr4:95409749-95410547	Hela-S3	cervix:	n/a	n/a
4	E2F4	chr4:95409774-95410545	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr4:95409734-95410383	A549	lung:	n/a	n/a
6	EP300	chr4:95409782-95410616	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr4:95409732-95410187	SK-N-MC	brain:	n/a	n/a
8	TFAP2C	chr4:95409652-95410234	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr4:95408960-95411285	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr4:95409741-95410714	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr4:95409758-95410685	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr4:95409772-95410380	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr4:95409794-95410471	Hela-S3	cervix:	n/a	n/a
14	TFAP2A	chr4:95409690-95410234	Hela-S3	cervix:	n/a	chr4:95409901-95409916
15	MAX	chr4:95409734-95410283	A549	lung:	n/a	n/a
16	MAX	chr4:95409760-95410250	Hela-S3	cervix:	n/a	n/a
17	MYC	chr4:95409662-95410703	MCF10A-Er-Src	breast:	n/a	chr4:95409721-95409730
18	RAD21	chr4:95409768-95410301	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr4:95409762-95410509	HUVEC	blood vessel:	n/a	n/a
20	CEBPB	chr4:95409751-95410659	Hela-S3	cervix:	n/a	n/a
21	GATA3	chr4:95409769-95410111	T-47D	breast:	n/a	chr4:95410098-95410105
22	TCF12	chr4:95409769-95410313	A549	lung:	n/a	n/a
23	STAT3	chr4:95409724-95410620	MCF10A-Er-Src	breast:	n/a	n/a
24	NFYB	chr4:95409788-95410142	Hela-S3	cervix:	n/a	n/a
25	MXI1	chr4:95409780-95410259	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr4:95408889-95411285	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr4:95409744-95410635	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr4:95409730-95410616	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr4:95409768-95410706	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr4:95409780-95410217	Hela-S3	cervix:	n/a	n/a
31	EP300	chr4:95409740-95410266	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95372926..95375393-chr4:95409110..95411441,2	MCF-7	breast:
2	chr4:95395769..95400285-chr4:95406149..95409946,5	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1353044	0.87[GIH][hapmap];0.92[MEX][hapmap]
rs2433317	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2433318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433325	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2438141	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438142	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2438144	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2438145	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2452556	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452557	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2452559	0.85[ASN][1000 genomes]
rs2452560	0.85[ASN][1000 genomes]
rs2452561	0.83[ASN][1000 genomes]
rs2452562	0.85[ASN][1000 genomes]
rs2452564	0.85[ASN][1000 genomes]
rs2452565	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2452566	0.82[ASN][1000 genomes]
rs2510785	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2510788	0.87[GIH][hapmap]
rs2510791	0.83[ASN][1000 genomes]
rs2510792	0.85[ASN][1000 genomes]
rs2510794	0.85[ASN][1000 genomes]
rs2510795	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2510798	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2510799	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510801	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510803	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2510804	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95387400-95410000	Weak transcription	NHLF	lung
3	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:95396800-95410000	Weak transcription	Fetal Intestine Large	intestine
8	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
9	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:95400800-95440000	Weak transcription	Lung	lung
11	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
13	chr4:95402200-95412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:95402200-95412200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:95402200-95412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
17	chr4:95403800-95417800	Weak transcription	HepG2	liver
18	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:95404400-95412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:95406000-95410200	Enhancers	HMEC	breast
22	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
23	chr4:95406200-95410600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr4:95406400-95410000	Weak transcription	HSMMtube	muscle
25	chr4:95406400-95411800	Weak transcription	HSMM	muscle
26	chr4:95407200-95410600	Enhancers	Fetal Heart	heart
27	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
28	chr4:95407600-95410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:95408000-95410000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:95408000-95410400	Enhancers	Psoas Muscle	Psoas
31	chr4:95408000-95412200	Weak transcription	Right Ventricle	heart
32	chr4:95408000-95412600	Weak transcription	Stomach Mucosa	stomach
33	chr4:95408000-95428000	Weak transcription	K562	blood
34	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:95408400-95410600	Enhancers	Hela-S3	cervix
36	chr4:95408600-95411000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:95408800-95410200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:95409000-95410400	Enhancers	NH-A	brain
39	chr4:95409000-95410600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:95409000-95410600	Enhancers	NHDF-Ad	bronchial
41	chr4:95409000-95412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:95409000-95422000	Weak transcription	Ovary	ovary
43	chr4:95409200-95410400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:95409200-95410600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:95409200-95411600	Weak transcription	Liver	Liver
46	chr4:95409400-95410000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:95409400-95410000	Weak transcription	Right Atrium	heart
48	chr4:95409400-95410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:95409400-95410600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:95409400-95412200	Enhancers	HUVEC	blood vessel

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