Variant report

Variant	rs3813659
Chromosome Location	chr2:96812819-96812820
allele	G/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	GATA1	chr2:96812580-96813284	K562	blood:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812929-96812936
2	GATA3	chr2:96811975-96813622	SK-N-SH	brain:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
3	POLR2A	chr2:96811687-96812909	GM12878	blood:	n/a	n/a
4	CCNT2	chr2:96812737-96813156	K562	blood:	n/a	n/a
5	SIN3AK20	chr2:96812717-96813122	SK-N-SH	brain:	n/a	n/a
6	USF2	chr2:96812627-96813562	Hela-S3	cervix:	n/a	n/a
7	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
8	TEAD4	chr2:96812504-96813274	SK-N-SH	brain:	n/a	n/a
9	MAX	chr2:96812561-96813240	SK-N-SH	brain:	n/a	n/a
10	EP300	chr2:96812642-96813141	SK-N-SH_RA	brain:	n/a	n/a
11	GATA3	chr2:96812494-96813461	MCF-7	breast:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
12	EP300	chr2:96812052-96813316	SK-N-SH	brain:	n/a	chr2:96812145-96812161 chr2:96812146-96812162
13	SMC3	chr2:96812606-96813056	Hela-S3	cervix:	n/a	n/a
14	RELA	chr2:96809062-96812996	GM19193	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
15	FOSL2	chr2:96812552-96813214	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:96812575-96813155	SK-N-SH	brain:	n/a	n/a
17	MYC	chr2:96809973-96813599	Hela-S3	cervix:	n/a	chr2:96811287-96811296 chr2:96812004-96812014
18	REST	chr2:96812701-96813220	MCF-7	breast:	n/a	chr2:96813022-96813035 chr2:96813022-96813035 chr2:96813019-96813032
19	POLR2A	chr2:96806742-96812863	Raji	blood:	n/a	n/a
20	EP300	chr2:96810859-96812900	GM12878	blood:	n/a	chr2:96812145-96812161 chr2:96812146-96812162 chr2:96811182-96811198
21	EP300	chr2:96811760-96815004	SK-N-SH	brain:	n/a	chr2:96813968-96813982 chr2:96812145-96812161 chr2:96812146-96812162
22	TBP	chr2:96812654-96813439	Hela-S3	cervix:	n/a	n/a
23	ELK1	chr2:96812549-96813119	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr2:96812754-96813062	T-47D	breast:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
25	RELA	chr2:96810788-96813081	GM18526	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
26	PML	chr2:96806496-96814786	GM12878	blood:	n/a	chr2:96814389-96814398
27	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
28	TFAP2C	chr2:96811756-96813708	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:96806166-96813187	GM19193	blood:	n/a	n/a
30	GATA3	chr2:96812396-96813264	SH-SY5Y	brain:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
31	GATA3	chr2:96812688-96813090	T-47D	breast:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
32	NFATC1	chr2:96806082-96812882	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:96797189-96814534	GM12892	blood:	n/a	n/a
34	MTA3	chr2:96812764-96813263	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:96812664-96813116	Hela-S3	cervix:	n/a	n/a
36	JUND	chr2:96812802-96813330	K562	blood:	n/a	n/a
37	PAX5	chr2:96811622-96812851	GM12878	blood:	n/a	chr2:96811906-96811924
38	MTA3	chr2:96806625-96815107	GM12878	blood:	n/a	n/a
39	EP300	chr2:96812318-96813308	SK-N-SH	brain:	n/a	n/a
40	SMARCB1	chr2:96809096-96813054	Hela-S3	cervix:	n/a	n/a
41	TEAD4	chr2:96812485-96813265	SK-N-SH	brain:	n/a	n/a
42	RAD21	chr2:96812700-96813074	SK-N-SH_RA	brain:	n/a	n/a
43	HMGN3	chr2:96812766-96813193	K562	blood:	n/a	n/a
44	POLR2A	chr2:96806534-96814566	GM12891	blood:	n/a	n/a
45	POLR2A	chr2:96802751-96813556	GM12892	blood:	n/a	n/a
46	KAP1	chr2:96812525-96814932	HEK293	kidney:	n/a	chr2:96814389-96814398
47	POLR2A	chr2:96806527-96812996	GM12891	blood:	n/a	n/a
48	YY1	chr2:96812808-96813072	SK-N-SH_RA	brain:	n/a	n/a
49	POLR2A	chr2:96812711-96813011	SK-N-SH	brain:	n/a	n/a
50	EBF1	chr2:96810831-96812924	GM12878	blood:	n/a	chr2:96811983-96811994 chr2:96811956-96811967

No.	Distal block	Cell Line	Cell type
1	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
2	chr2:96781942..96784647-chr2:96809826..96814461,4	MCF-7	breast:
3	chr2:96812496..96814407-chr2:96931175..96932948,2	MCF-7	breast:
4	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:

Variant related genes	Relation type
DUSP2	TF binding region
ENSG00000228873	TF binding region
ENSG00000222040	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12611936	1.00[AMR][1000 genomes]
rs12612136	1.00[AMR][1000 genomes]
rs12614113	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12614623	1.00[AMR][1000 genomes]
rs12616326	1.00[AMR][1000 genomes]
rs12619114	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12619490	1.00[AMR][1000 genomes]
rs12619573	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12620576	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12620768	1.00[AMR][1000 genomes]
rs12621163	1.00[AMR][1000 genomes]
rs12621619	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12621688	1.00[AMR][1000 genomes]
rs2276647	1.00[AMR][1000 genomes]
rs2290908	1.00[AMR][1000 genomes]
rs3813660	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57319731	1.00[AMR][1000 genomes]
rs57367779	1.00[AMR][1000 genomes]
rs57477571	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58132887	1.00[AMR][1000 genomes]
rs59168739	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59525841	1.00[AMR][1000 genomes]
rs59621486	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59911784	1.00[AMR][1000 genomes]
rs60013962	1.00[AMR][1000 genomes]
rs60020980	1.00[AMR][1000 genomes]
rs60596893	1.00[AMR][1000 genomes]
rs60893927	1.00[AMR][1000 genomes]
rs61096003	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
14	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
17	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
18	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96809600-96813000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:96810000-96815000	Enhancers	Fetal Heart	heart
3	chr2:96810400-96813000	Flanking Active TSS	Dnd41	blood
4	chr2:96810400-96815000	Enhancers	Fetal Lung	lung
5	chr2:96811200-96814000	Weak transcription	HUVEC	blood vessel
6	chr2:96811200-96814400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:96811200-96814400	Weak transcription	Gastric	stomach
8	chr2:96811200-96814600	Enhancers	Spleen	Spleen
9	chr2:96811200-96814800	Enhancers	Lung	lung
10	chr2:96811200-96815000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:96811200-96815000	Enhancers	NH-A	brain
12	chr2:96811200-96815200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:96811400-96813000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:96811400-96813000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:96811400-96813000	Enhancers	Brain Hippocampus Middle	brain
16	chr2:96811400-96813000	Flanking Active TSS	GM12878-XiMat	blood
17	chr2:96811400-96813200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr2:96811400-96813400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:96811400-96814200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr2:96811400-96814200	Weak transcription	A549	lung
21	chr2:96811400-96814400	Enhancers	Right Atrium	heart
22	chr2:96811400-96814600	Enhancers	Osteobl	bone
23	chr2:96811400-96814800	Flanking Active TSS	Fetal Thymus	thymus
24	chr2:96811400-96815000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:96811400-96815200	Flanking Active TSS	Hela-S3	cervix
26	chr2:96811600-96813000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:96811600-96813200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr2:96811600-96813200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:96811600-96813400	Bivalent Enhancer	Placenta	Placenta
30	chr2:96811600-96813800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr2:96811600-96813800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:96811600-96813800	Enhancers	Brain Anterior Caudate	brain
33	chr2:96811600-96814000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:96811600-96814200	Weak transcription	Pancreas	Pancrea
35	chr2:96811600-96814400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:96811600-96814600	Enhancers	Left Ventricle	heart
37	chr2:96811600-96814600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:96811600-96815000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr2:96811600-96815000	Enhancers	Right Ventricle	heart
42	chr2:96811600-96815000	Enhancers	HMEC	breast
43	chr2:96811600-96815200	Enhancers	Fetal Stomach	stomach
44	chr2:96811800-96813200	Weak transcription	Fetal Kidney	kidney
45	chr2:96811800-96814200	Enhancers	Colonic Mucosa	Colon
46	chr2:96811800-96814400	Enhancers	K562	blood
47	chr2:96811800-96814800	Enhancers	Adipose Nuclei	Adipose
48	chr2:96811800-96815000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:96811800-96815200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:96812000-96813600	Weak transcription	Stomach Smooth Muscle	stomach

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