Variant report

Variant	rs2510802
Chromosome Location	chr4:95410168-95410169
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	ELK1	chr4:95409809-95410269	Hela-S3	cervix:	n/a	n/a
6	MAX	chr4:95409734-95410383	A549	lung:	n/a	n/a
7	EP300	chr4:95409782-95410616	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr4:95409732-95410187	SK-N-MC	brain:	n/a	n/a
9	TFAP2C	chr4:95409652-95410234	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr4:95408960-95411285	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr4:95409741-95410714	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr4:95409758-95410685	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr4:95409899-95410583	IMR90	lung:	n/a	n/a
14	MYC	chr4:95409772-95410380	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr4:95409812-95410704	MCF10A-Er-Src	breast:	n/a	n/a
16	GTF2F1	chr4:95409838-95410288	Hela-S3	cervix:	n/a	n/a
17	STAT3	chr4:95409794-95410471	Hela-S3	cervix:	n/a	n/a
18	USF2	chr4:95409893-95410181	Hela-S3	cervix:	n/a	n/a
19	TFAP2A	chr4:95409690-95410234	Hela-S3	cervix:	n/a	chr4:95409901-95409916
20	SMC3	chr4:95409807-95410397	Hela-S3	cervix:	n/a	n/a
21	MAFK	chr4:95409836-95410228	IMR90	lung:	n/a	n/a
22	MAX	chr4:95409734-95410283	A549	lung:	n/a	n/a
23	GABPA	chr4:95409837-95410284	A549	lung:	n/a	n/a
24	ELF1	chr4:95409808-95410237	MCF-7	breast:	n/a	n/a
25	MAX	chr4:95409760-95410250	Hela-S3	cervix:	n/a	n/a
26	MYC	chr4:95409662-95410703	MCF10A-Er-Src	breast:	n/a	chr4:95409721-95409730
27	RAD21	chr4:95409768-95410301	Hela-S3	cervix:	n/a	n/a
28	FOSL2	chr4:95409817-95410288	A549	lung:	n/a	n/a
29	FOXA1	chr4:95409844-95410172	T-47D	breast:	n/a	n/a
30	POLR2A	chr4:95409762-95410509	HUVEC	blood vessel:	n/a	n/a
31	ELK4	chr4:95409907-95410265	Hela-S3	cervix:	n/a	n/a
32	TAF1	chr4:95409961-95410205	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr4:95409751-95410659	Hela-S3	cervix:	n/a	n/a
34	SP1	chr4:95409823-95410287	A549	lung:	n/a	chr4:95409962-95409983
35	KAP1	chr4:95409936-95410208	U2OS	brain:	n/a	n/a
36	TCF12	chr4:95409769-95410313	A549	lung:	n/a	n/a
37	CHD2	chr4:95409979-95410308	Hela-S3	cervix:	n/a	n/a
38	STAT3	chr4:95409724-95410620	MCF10A-Er-Src	breast:	n/a	n/a
39	RCOR1	chr4:95409847-95410443	Hela-S3	cervix:	n/a	n/a
40	MXI1	chr4:95409780-95410259	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr4:95408889-95411285	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr4:95409744-95410635	MCF10A-Er-Src	breast:	n/a	n/a
43	STAT3	chr4:95409730-95410616	MCF10A-Er-Src	breast:	n/a	n/a
44	RFX5	chr4:95409914-95410537	Hela-S3	cervix:	n/a	n/a
45	MAFK	chr4:95409859-95410560	Hela-S3	cervix:	n/a	n/a
46	FOS	chr4:95409822-95410663	MCF10A-Er-Src	breast:	n/a	n/a
47	SETDB1	chr4:95409910-95410241	U2OS	brain:	n/a	n/a
48	FOS	chr4:95409768-95410706	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr4:95409780-95410217	Hela-S3	cervix:	n/a	n/a
50	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:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1353044	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2433317	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2433318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433324	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2433325	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs2438141	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438142	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs2438144	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs2438145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452554	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]
rs2452556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452557	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452559	0.86[ASN][1000 genomes]
rs2452560	0.86[ASN][1000 genomes]
rs2452561	0.85[ASN][1000 genomes]
rs2452562	0.86[ASN][1000 genomes]
rs2452564	0.86[ASN][1000 genomes]
rs2452565	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2452566	0.84[ASN][1000 genomes]
rs2510785	0.80[CHD][hapmap];0.91[MEX][hapmap]
rs2510788	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs2510791	0.84[ASN][1000 genomes]
rs2510792	0.86[ASN][1000 genomes]
rs2510794	0.86[ASN][1000 genomes]
rs2510795	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2510798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2510799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510803	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2510804	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[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:66 , 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	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
7	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:95400800-95440000	Weak transcription	Lung	lung
9	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
11	chr4:95402200-95412000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:95402200-95412200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:95402200-95412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
15	chr4:95403800-95417800	Weak transcription	HepG2	liver
16	chr4:95404000-95415000	Weak transcription	Fetal Intestine Small	intestine
17	chr4:95404400-95412200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:95406000-95410200	Enhancers	HMEC	breast
20	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
21	chr4:95406200-95410600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:95406400-95411800	Weak transcription	HSMM	muscle
23	chr4:95407200-95410600	Enhancers	Fetal Heart	heart
24	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
25	chr4:95407600-95410200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:95408000-95410400	Enhancers	Psoas Muscle	Psoas
27	chr4:95408000-95412200	Weak transcription	Right Ventricle	heart
28	chr4:95408000-95412600	Weak transcription	Stomach Mucosa	stomach
29	chr4:95408000-95428000	Weak transcription	K562	blood
30	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:95408400-95410600	Enhancers	Hela-S3	cervix
32	chr4:95408600-95411000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:95408800-95410200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:95409000-95410400	Enhancers	NH-A	brain
35	chr4:95409000-95410600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr4:95409000-95410600	Enhancers	NHDF-Ad	bronchial
37	chr4:95409000-95412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:95409000-95422000	Weak transcription	Ovary	ovary
39	chr4:95409200-95410400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:95409200-95410600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:95409200-95411600	Weak transcription	Liver	Liver
42	chr4:95409400-95410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:95409400-95410600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:95409400-95412200	Enhancers	HUVEC	blood vessel
45	chr4:95409400-95419000	Weak transcription	Aorta	Aorta
46	chr4:95409800-95410200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:95409800-95410200	Enhancers	Fetal Muscle Leg	muscle
48	chr4:95409800-95410200	Active TSS	NHEK	skin
49	chr4:95409800-95410400	Enhancers	Colon Smooth Muscle	Colon
50	chr4:95409800-95410600	Enhancers	Muscle Satellite Cultured Cells	--

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