Variant report

Variant	rs17487596
Chromosome Location	chr5:96269407-96269408
allele	A/G
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	POLR2A	chr5:96269126-96273104	GM12892	blood:	n/a	n/a
2	POLR2A	chr5:96268968-96273188	GM12878	blood:	n/a	n/a
3	CHD1	chr5:96267264-96273025	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:96269090-96273351	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:96269401-96273113	GM12892	blood:	n/a	n/a
6	POLR2A	chr5:96267158-96273083	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:96269159-96273111	GM19099	blood:	n/a	n/a
8	NFATC1	chr5:96269097-96271957	GM12878	blood:	n/a	n/a
9	MTA3	chr5:96269032-96271945	GM12878	blood:	n/a	n/a
10	CEBPB	chr5:96269247-96272002	GM12878	blood:	n/a	chr5:96269489-96269502
11	EP300	chr5:96269245-96271893	GM12878	blood:	n/a	chr5:96271529-96271545
12	POLR2A	chr5:96269191-96273111	GM12891	blood:	n/a	n/a
13	MAZ	chr5:96269392-96269471	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:96268644-96272934	GM12892	blood:	n/a	n/a
15	GATA1	chr5:96267929-96269867	PBDE	blood:	n/a	chr5:96268501-96268511 chr5:96268719-96268740
16	PML	chr5:96266960-96273172	GM12878	blood:	n/a	n/a
17	ZNF384	chr5:96268617-96269442	GM12878	blood:	n/a	n/a
18	EP300	chr5:96269287-96271884	K562	blood:	n/a	chr5:96271529-96271545
19	ATF2	chr5:96269349-96271908	GM12878	blood:	n/a	n/a
20	SMC3	chr5:96269323-96269800	GM12878	blood:	n/a	n/a
21	MXI1	chr5:96269224-96273218	SK-N-SH	brain:	n/a	n/a
22	RELA	chr5:96269287-96271962	GM10847	blood:	n/a	chr5:96271574-96271583 chr5:96271574-96271583
23	POLR2A	chr5:96269078-96273100	GM12891	blood:	n/a	n/a
24	POLR2A	chr5:96268685-96273087	GM12891	blood:	n/a	n/a
25	POLR2A	chr5:96268814-96273013	Raji	blood:	n/a	n/a
26	E2F4	chr5:96269302-96269540	MCF10A-Er-Src	breast:	n/a	n/a
27	ATF2	chr5:96269341-96272020	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:96268990-96273112	GM12891	blood:	n/a	n/a
29	GATA1	chr5:96267043-96269474	K562	blood:	n/a	chr5:96268501-96268511 chr5:96268719-96268740
30	BCLAF1	chr5:96269281-96272131	GM12878	blood:	n/a	chr5:96271575-96271584 chr5:96271542-96271555
31	POLR2A	chr5:96269196-96273040	GM18951	blood:	n/a	n/a
32	RELA	chr5:96269090-96271931	GM18505	blood:	n/a	chr5:96271574-96271583 chr5:96271574-96271583
33	MXI1	chr5:96269137-96273175	GM12878	blood:	n/a	n/a
34	CHD2	chr5:96269397-96271973	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:96268587-96273078	GM18505	blood:	n/a	n/a
36	NFIC	chr5:96269246-96272062	GM12878	blood:	n/a	n/a
37	EP300	chr5:96269226-96269426	GM12878	blood:	n/a	n/a
38	TBP	chr5:96269284-96271905	GM12878	blood:	n/a	n/a
39	POLR2A	chr5:96268807-96273159	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:96268818-96273031	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:96269367-96272814	GM18526	blood:	n/a	n/a
42	POLR2A	chr5:96268850-96273070	GM12892	blood:	n/a	n/a
43	POLR2A	chr5:96269156-96272033	GM12892	blood:	n/a	n/a
44	POLR2A	chr5:96269345-96269442	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr5:96269396-96271891	K562	blood:	n/a	n/a
46	MTA3	chr5:96268487-96273163	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96267069..96273023-chr5:96293959..96302488,9	K562	blood:
2	chr5:96140726..96144602-chr5:96269258..96273227,6	MCF-7	breast:
3	chr5:96269264..96270961-chr5:96303630..96305145,2	MCF-7	breast:
4	chr5:96210744..96214555-chr5:96268958..96271606,4	MCF-7	breast:
5	chr5:96268592..96270496-chr5:96515475..96517242,2	MCF-7	breast:
6	chr5:96268234..96272758-chr5:96290815..96294670,4	K562	blood:
7	chr5:96087767..96089736-chr5:96268436..96270992,2	MCF-7	breast:
8	chr5:96268127..96270774-chr5:96299213..96300719,2	K562	blood:
9	chr5:96268279..96270263-chr5:96284683..96286210,2	K562	blood:
10	chr5:96207193..96215079-chr5:96269183..96273335,11	MCF-7	breast:
11	chr5:96141925..96145850-chr5:96265867..96272606,9	K562	blood:
12	chr5:96268650..96270760-chr5:96289002..96291090,2	MCF-7	breast:

Variant related genes	Relation type
LNPEP	TF binding region
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000164308	Chromatin interaction
ENSG00000272109	Chromatin interaction
ENSG00000164307	Chromatin interaction
ENSG00000200884	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10491385	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10491386	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10515253	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1057808	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1134681	0.89[AMR][1000 genomes]
rs17087180	0.89[AMR][1000 genomes]
rs17407513	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17407871	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17407899	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17408150	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17409040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17446635	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17446755	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17446769	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17446837	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17446907	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17446949	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17486181	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17486481	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs17486509	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17486775	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17486915	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17487132	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17531068	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531164	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531192	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531213	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17531366	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17628359	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17684739	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3797797	1.00[AFR][1000 genomes]
rs41276275	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41276279	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55658367	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55746248	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55767008	1.00[AFR][1000 genomes]
rs55769558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55870170	1.00[AFR][1000 genomes]
rs56002769	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56003936	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56009267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56071818	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56078010	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6862437	0.89[AMR][1000 genomes]
rs6883674	0.89[AMR][1000 genomes]
rs6883859	0.89[AMR][1000 genomes]
rs7714122	0.89[AMR][1000 genomes]
rs7719293	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7721014	0.89[AMR][1000 genomes]
rs7728999	0.89[AMR][1000 genomes]
rs7729489	0.89[AMR][1000 genomes]
rs7733301	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96229600-96269600	Weak transcription	Aorta	Aorta
2	chr5:96229800-96270000	Weak transcription	Esophagus	oesophagus
3	chr5:96246000-96270200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:96249800-96270000	Weak transcription	Lung	lung
5	chr5:96257400-96269600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:96265000-96270000	Weak transcription	Pancreas	Pancrea
7	chr5:96265400-96270000	Weak transcription	Left Ventricle	heart
8	chr5:96267000-96269600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:96267000-96269600	Enhancers	Fetal Lung	lung
10	chr5:96267600-96270400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr5:96267800-96270000	Flanking Active TSS	Dnd41	blood
12	chr5:96267800-96270200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr5:96267800-96270400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr5:96267800-96270600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:96268200-96269600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:96268200-96269600	Enhancers	Hela-S3	cervix
17	chr5:96268200-96269600	Enhancers	NHEK	skin
18	chr5:96268200-96270200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr5:96268200-96270400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr5:96268200-96274000	Active TSS	GM12878-XiMat	blood
21	chr5:96268400-96270400	Weak transcription	Gastric	stomach
22	chr5:96268400-96270400	Weak transcription	Spleen	Spleen
23	chr5:96268400-96271200	Active TSS	Primary T cells fromperipheralblood	blood
24	chr5:96268400-96272600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:96268400-96273400	Active TSS	Fetal Thymus	thymus
26	chr5:96268400-96273600	Active TSS	Thymus	Thymus
27	chr5:96268600-96269600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:96268600-96270200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr5:96268600-96270200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr5:96268800-96269800	Enhancers	Small Intestine	intestine
31	chr5:96269000-96269600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:96269000-96269600	Enhancers	Fetal Muscle Leg	muscle
33	chr5:96269000-96269800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr5:96269000-96270000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:96269000-96270200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:96269000-96270200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr5:96269000-96270200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:96269000-96270200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr5:96269000-96270600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:96269200-96269600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:96269200-96269600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:96269200-96269600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:96269200-96269600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr5:96269200-96269600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:96269200-96269600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:96269200-96269600	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr5:96269200-96269600	Enhancers	HSMM	muscle
48	chr5:96269200-96269600	Enhancers	HSMMtube	muscle
49	chr5:96269200-96269600	Enhancers	Osteobl	bone
50	chr5:96269200-96269800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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