Variant report

Variant	rs2702323
Chromosome Location	chr4:56815880-56815881
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	MAZ	chr4:56814698-56816093	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:56813158-56816168	HUVEC	blood vessel:	n/a	n/a
3	RCOR1	chr4:56813365-56815980	GM12878	blood:	n/a	n/a
4	MAX	chr4:56814675-56816543	NB4	blood:	n/a	n/a
5	ARID3A	chr4:56815523-56816127	HepG2	liver:	n/a	chr4:56815625-56815641
6	RELA	chr4:56813238-56816761	GM12891	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
7	MTA3	chr4:56813232-56816058	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:56814639-56816056	GM19193	blood:	n/a	n/a
9	PML	chr4:56813219-56815891	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:56813356-56816455	GM12892	blood:	n/a	n/a
11	POLR2A	chr4:56814702-56815972	HepG2	liver:	n/a	n/a
12	POLR2A	chr4:56813984-56816308	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr4:56814279-56816206	NB4	blood:	n/a	n/a
14	MXI1	chr4:56814131-56816737	SK-N-SH	brain:	n/a	chr4:56815054-56815069 chr4:56815052-56815067
15	RELA	chr4:56813567-56816431	GM12892	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
16	POLR2A	chr4:56813317-56816266	IMR90	lung:	n/a	n/a
17	CHD1	chr4:56813363-56816295	GM12878	blood:	n/a	chr4:56815368-56815378 chr4:56814858-56814868
18	POLR2A	chr4:56814702-56815916	HUVEC	blood vessel:	n/a	n/a
19	FOXA1	chr4:56815160-56815938	HepG2	liver:	n/a	chr4:56815777-56815792
20	EP300	chr4:56814760-56816086	K562	blood:	n/a	chr4:56814943-56814952 chr4:56814919-56814935 chr4:56814926-56814935
21	POLR2A	chr4:56813123-56816170	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:56814698-56816003	K562	blood:	n/a	n/a
23	HCFC1	chr4:56814086-56816232	Hela-S3	cervix:	n/a	n/a
24	RELA	chr4:56813325-56816613	GM10847	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
25	E2F4	chr4:56814365-56816301	MCF10A-Er-Src	breast:	n/a	n/a
26	RUNX3	chr4:56814640-56815890	GM12878	blood:	n/a	chr4:56815742-56815757
27	YY1	chr4:56814721-56815928	SK-N-SH_RA	brain:	n/a	chr4:56815321-56815335 chr4:56815103-56815120
28	RUNX3	chr4:56814503-56815945	GM12878	blood:	n/a	chr4:56815742-56815757
29	RAD21	chr4:56813571-56816650	SK-N-SH	brain:	n/a	chr4:56813922-56813935 chr4:56814940-56814952 chr4:56813920-56813934 chr4:56814940-56814950 chr4:56814938-56814951 chr4:56813919-56813938 chr4:56814919-56814932 chr4:56814935-56814954
30	MAZ	chr4:56813259-56816748	IMR90	lung:	n/a	n/a
31	MXI1	chr4:56814199-56816503	IMR90	lung:	n/a	chr4:56815054-56815069 chr4:56815052-56815067
32	EP300	chr4:56815482-56815908	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:56813263-56816279	GM19099	blood:	n/a	n/a
34	RELA	chr4:56813320-56816350	GM15510	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
35	POLR2A	chr4:56813156-56815885	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr4:56814599-56815897	HCT-116	colon:	n/a	n/a
37	RELA	chr4:56813252-56816466	GM19099	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
38	POLR2A	chr4:56814340-56816222	ProgFib	skin:	n/a	n/a
39	CEBPB	chr4:56814253-56816046	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr4:56813240-56816522	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:56813224-56816657	GM12891	blood:	n/a	n/a
42	MYC	chr4:56815804-56815984	MCF10A-Er-Src	breast:	n/a	n/a
43	IRF1	chr4:56814876-56815904	K562	blood:	n/a	chr4:56815341-56815350
44	GATA1	chr4:56814487-56816211	PBDE	blood:	n/a	chr4:56815339-56815349
45	POLR2A	chr4:56814697-56815902	H1-hESC	embryonic stem cell:	n/a	n/a
46	RELA	chr4:56813262-56816441	GM18505	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
47	POLR2A	chr4:56813305-56816080	Raji	blood:	n/a	n/a
48	SMC3	chr4:56814050-56816161	SK-N-SH	brain:	n/a	chr4:56814940-56814950 chr4:56814936-56814950
49	POLR2A	chr4:56814187-56816361	Hela-S3	cervix:	n/a	n/a
50	STAT3	chr4:56815803-56815881	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56813951..56816639-chr4:57299941..57302593,2	K562	blood:
2	chr4:56815034..56815908-chr7:152373038..152373850,2	Hela-S3	cervix:
3	chr4:56246727..56248649-chr4:56813928..56816601,2	K562	blood:
4	chr4:56815530..56818223-chr4:56910044..56912161,2	K562	blood:
5	chr4:56813904..56818311-chr4:57252529..57254894,5	K562	blood:
6	chr4:56794068..56796669-chr4:56814956..56816613,2	K562	blood:

Variant related genes	Relation type
CEP135	TF binding region
ENSG00000269921	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000196584	Chromatin interaction
ENSG00000222954	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10003765	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013329	1.00[CHB][hapmap]
rs10027961	1.00[CHB][hapmap]
rs17086086	1.00[CHB][hapmap]
rs17086122	1.00[CHB][hapmap]
rs2593067	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593084	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593087	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2611824	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2611825	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2611827	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2702326	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2702331	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2702343	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2702346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2702348	1.00[CHB][hapmap]
rs2702350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2702358	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41467652	1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs719007	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56812200-56816200	Active TSS	Lung	lung
2	chr4:56812600-56816000	Active TSS	Left Ventricle	heart
3	chr4:56812600-56816200	Active TSS	Right Ventricle	heart
4	chr4:56813000-56816800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:56813200-56816000	Active TSS	Psoas Muscle	Psoas
6	chr4:56813200-56816000	Active TSS	Right Atrium	heart
7	chr4:56813400-56816000	Active TSS	Fetal Intestine Small	intestine
8	chr4:56813400-56816200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:56813400-56816200	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:56813400-56816800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:56813600-56819200	Active TSS	GM12878-XiMat	blood
12	chr4:56813800-56816000	Active TSS	Aorta	Aorta
13	chr4:56813800-56816000	Active TSS	Ovary	ovary
14	chr4:56813800-56816200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:56814000-56816200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:56814000-56816200	Active TSS	HSMMtube	muscle
17	chr4:56814200-56816200	Active TSS	A549	lung
18	chr4:56814400-56816200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr4:56814400-56816200	Active TSS	HSMM	muscle
20	chr4:56814400-56816200	Active TSS	NHDF-Ad	bronchial
21	chr4:56814600-56816000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:56814600-56816000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:56814600-56816200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:56814600-56816200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:56814600-56816200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:56814600-56816200	Active TSS	Fetal Brain Female	brain
27	chr4:56814600-56816400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr4:56814600-56816400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:56814600-56816400	Active TSS	NHLF	lung
30	chr4:56814600-56816600	Active TSS	H1 Cell Line	embryonic stem cell
31	chr4:56814600-56816600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr4:56814800-56816000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:56814800-56816000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr4:56814800-56816000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:56814800-56816000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:56814800-56816000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:56814800-56816000	Active TSS	Muscle Satellite Cultured Cells	--
38	chr4:56814800-56816000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:56814800-56816000	Active TSS	Fetal Intestine Large	intestine
40	chr4:56814800-56816000	Active TSS	Placenta	Placenta
41	chr4:56814800-56816000	Active TSS	Hela-S3	cervix
42	chr4:56814800-56816000	Active TSS	Osteobl	bone
43	chr4:56814800-56816200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:56814800-56816200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr4:56814800-56816200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:56814800-56816200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:56814800-56816200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:56814800-56816200	Bivalent/Poised TSS	HepG2	liver
49	chr4:56814800-56816200	Active TSS	K562	blood
50	chr4:56814800-56816400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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