Variant report

Variant	rs3813660
Chromosome Location	chr2:96812221-96812222
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	GATA3	chr2:96811975-96813622	SK-N-SH	brain:	n/a	chr2:96812929-96812938 chr2:96812928-96812938 chr2:96812928-96812936 chr2:96812929-96812936
2	EP300	chr2:96812104-96812401	GM12878	blood:	n/a	chr2:96812145-96812161 chr2:96812146-96812162
3	POLR2A	chr2:96806257-96812804	GM15510	blood:	n/a	n/a
4	POU2F2	chr2:96811607-96812556	GM12891	blood:	n/a	chr2:96811752-96811764
5	ZEB1	chr2:96812022-96812430	GM12878	blood:	n/a	chr2:96812258-96812267 chr2:96812256-96812267
6	TAF1	chr2:96811669-96812704	GM12878	blood:	n/a	n/a
7	SPI1	chr2:96811604-96812744	GM12878	blood:	n/a	chr2:96812085-96812098 chr2:96811747-96811760
8	POLR2A	chr2:96811687-96812909	GM12878	blood:	n/a	n/a
9	GABPA	chr2:96812124-96812330	K562	blood:	n/a	n/a
10	STAT3	chr2:96810990-96812733	GM12878	blood:	n/a	chr2:96811748-96811760 chr2:96811324-96811336 chr2:96811753-96811765
11	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
12	SMC3	chr2:96811821-96812703	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:96812048-96812310	Hela-S3	cervix:	n/a	n/a
14	FOXM1	chr2:96810717-96812737	GM12878	blood:	n/a	n/a
15	EP300	chr2:96812052-96813316	SK-N-SH	brain:	n/a	chr2:96812145-96812161 chr2:96812146-96812162
16	RELA	chr2:96809062-96812996	GM19193	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
17	TBL1XR1	chr2:96807840-96812802	GM12878	blood:	n/a	n/a
18	MYC	chr2:96809973-96813599	Hela-S3	cervix:	n/a	chr2:96811287-96811296 chr2:96812004-96812014
19	MEF2A	chr2:96811807-96812538	GM12878	blood:	n/a	n/a
20	RFX5	chr2:96811872-96812689	GM12878	blood:	n/a	n/a
21	PAX5	chr2:96811714-96812663	GM12878	blood:	n/a	chr2:96811906-96811924
22	IRF4	chr2:96811851-96812649	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:96806742-96812863	Raji	blood:	n/a	n/a
24	EP300	chr2:96810859-96812900	GM12878	blood:	n/a	chr2:96812145-96812161 chr2:96812146-96812162 chr2:96811182-96811198
25	EP300	chr2:96811760-96815004	SK-N-SH	brain:	n/a	chr2:96813968-96813982 chr2:96812145-96812161 chr2:96812146-96812162
26	POLR2A	chr2:96812107-96812315	K562	blood:	n/a	n/a
27	TCF3	chr2:96811831-96812566	GM12878	blood:	n/a	n/a
28	NRF1	chr2:96810914-96812492	GM12878	blood:	n/a	n/a
29	RXRA	chr2:96811995-96812362	GM12878	blood:	n/a	chr2:96812301-96812308
30	RELA	chr2:96810788-96813081	GM18526	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
31	PML	chr2:96806496-96814786	GM12878	blood:	n/a	chr2:96814389-96814398
32	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
33	ETS1	chr2:96811794-96812520	GM12878	blood:	n/a	chr2:96812457-96812466
34	TFAP2C	chr2:96811756-96813708	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:96806166-96813187	GM19193	blood:	n/a	n/a
36	POU2F2	chr2:96811660-96812480	GM12878	blood:	n/a	chr2:96811752-96811764
37	POLR2A	chr2:96805990-96812814	GM12892	blood:	n/a	n/a
38	IRF3	chr2:96812111-96812458	GM12878	blood:	n/a	n/a
39	BCL11A	chr2:96811791-96812485	GM12878	blood:	n/a	chr2:96811971-96811980 chr2:96812149-96812162
40	PAX5	chr2:96811697-96812435	GM12892	blood:	n/a	chr2:96811906-96811924
41	TCF12	chr2:96811691-96812795	GM12878	blood:	n/a	chr2:96812258-96812265
42	NFATC1	chr2:96806082-96812882	GM12878	blood:	n/a	n/a
43	ETS1	chr2:96811968-96812500	GM12878	blood:	n/a	chr2:96812457-96812466
44	POLR2A	chr2:96797189-96814534	GM12892	blood:	n/a	n/a
45	PBX3	chr2:96812162-96812399	GM12878	blood:	n/a	n/a
46	BCL3	chr2:96811647-96812427	GM12878	blood:	n/a	chr2:96811971-96811980 chr2:96812149-96812162
47	EGR1	chr2:96812136-96812494	GM12878	blood:	n/a	n/a
48	IRF4	chr2:96811902-96812748	GM12878	blood:	n/a	n/a
49	ZNF384	chr2:96811899-96812455	GM12878	blood:	n/a	n/a
50	PAX5	chr2:96811622-96812851	GM12878	blood:	n/a	chr2:96811906-96811924

No.	Distal block	Cell Line	Cell type
1	chr2:96781378..96786213-chr2:96808688..96812498,6	MCF-7	breast:
2	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
3	chr2:96781942..96784647-chr2:96809826..96814461,4	MCF-7	breast:
4	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:

Variant related genes	Relation type
DUSP2	TF binding region
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000222040	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000135956	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[AFR][1000 genomes];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]
rs3813659	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:100 , 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	chr2:96809800-96812400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:96809800-96812600	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr2:96810000-96812600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr2:96810000-96815000	Enhancers	Fetal Heart	heart
6	chr2:96810200-96812600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:96810400-96812400	Active TSS	Thymus	Thymus
8	chr2:96810400-96813000	Flanking Active TSS	Dnd41	blood
9	chr2:96810400-96815000	Enhancers	Fetal Lung	lung
10	chr2:96810600-96812800	Enhancers	Stomach Mucosa	stomach
11	chr2:96811200-96812400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr2:96811200-96812600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr2:96811200-96812800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr2:96811200-96812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:96811200-96812800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr2:96811200-96814000	Weak transcription	HUVEC	blood vessel
17	chr2:96811200-96814400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:96811200-96814400	Weak transcription	Gastric	stomach
19	chr2:96811200-96814600	Enhancers	Spleen	Spleen
20	chr2:96811200-96814800	Enhancers	Lung	lung
21	chr2:96811200-96815000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:96811200-96815000	Enhancers	NH-A	brain
23	chr2:96811200-96815200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:96811400-96812400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr2:96811400-96812600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr2:96811400-96812600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:96811400-96812600	Flanking Active TSS	NHEK	skin
28	chr2:96811400-96812800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:96811400-96813000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:96811400-96813000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:96811400-96813000	Enhancers	Brain Hippocampus Middle	brain
32	chr2:96811400-96813000	Flanking Active TSS	GM12878-XiMat	blood
33	chr2:96811400-96813200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr2:96811400-96813400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:96811400-96814200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:96811400-96814200	Weak transcription	A549	lung
37	chr2:96811400-96814400	Enhancers	Right Atrium	heart
38	chr2:96811400-96814600	Enhancers	Osteobl	bone
39	chr2:96811400-96814800	Flanking Active TSS	Fetal Thymus	thymus
40	chr2:96811400-96815000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:96811400-96815200	Flanking Active TSS	Hela-S3	cervix
42	chr2:96811600-96812400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:96811600-96812400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:96811600-96812400	Weak transcription	Esophagus	oesophagus
45	chr2:96811600-96812600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:96811600-96812600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:96811600-96812600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr2:96811600-96812800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:96811600-96813000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:96811600-96813200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links