Variant report

Variant	rs2969489
Chromosome Location	chr2:96811434-96811435
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	chr2:96810155-96811572	H1-hESC	embryonic stem cell:	n/a	n/a
2	ELF1	chr2:96808984-96811640	GM12878	blood:	n/a	chr2:96811107-96811118 chr2:96811217-96811229
3	POLR2A	chr2:96806257-96812804	GM15510	blood:	n/a	n/a
4	CHD2	chr2:96810933-96811712	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr2:96809756-96812010	H1-hESC	embryonic stem cell:	n/a	chr2:96811126-96811138 chr2:96811127-96811134 chr2:96811127-96811134 chr2:96811127-96811134
6	E2F1	chr2:96810602-96811620	Hela-S3	cervix:	n/a	chr2:96811126-96811138 chr2:96811127-96811134 chr2:96811127-96811134 chr2:96811127-96811134
7	NFYA	chr2:96810868-96811581	Hela-S3	cervix:	n/a	n/a
8	SRF	chr2:96810814-96811589	HCT-116	colon:	n/a	chr2:96811229-96811247 chr2:96811230-96811247 chr2:96811232-96811245 chr2:96811233-96811247 chr2:96811231-96811246
9	TCF3	chr2:96810198-96811464	GM12878	blood:	n/a	n/a
10	MAX	chr2:96809846-96811548	HCT-116	colon:	n/a	chr2:96811287-96811296
11	MAZ	chr2:96809856-96811754	IMR90	lung:	n/a	chr2:96811287-96811296
12	YY1	chr2:96810671-96811519	GM12892	blood:	n/a	chr2:96811325-96811334 chr2:96811323-96811334
13	STAT3	chr2:96810990-96812733	GM12878	blood:	n/a	chr2:96811748-96811760 chr2:96811324-96811336 chr2:96811753-96811765
14	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
15	EGR1	chr2:96810850-96811496	GM12878	blood:	n/a	chr2:96811449-96811459
16	FOXM1	chr2:96810717-96812737	GM12878	blood:	n/a	n/a
17	YY1	chr2:96810658-96811440	GM12878	blood:	n/a	chr2:96811325-96811334 chr2:96811323-96811334
18	RELA	chr2:96809062-96812996	GM19193	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
19	ELK1	chr2:96810752-96811669	Hela-S3	cervix:	n/a	n/a
20	SRF	chr2:96810897-96811556	ECC-1	luminal epithelium:	n/a	chr2:96811229-96811247 chr2:96811230-96811247 chr2:96811232-96811245 chr2:96811233-96811247 chr2:96811231-96811246
21	TBL1XR1	chr2:96807840-96812802	GM12878	blood:	n/a	n/a
22	MYC	chr2:96809973-96813599	Hela-S3	cervix:	n/a	chr2:96811287-96811296 chr2:96812004-96812014
23	JUND	chr2:96811358-96811622	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F4	chr2:96810939-96811445	GM12878	blood:	n/a	chr2:96811126-96811138 chr2:96811127-96811134 chr2:96811127-96811134 chr2:96811127-96811134
25	POLR2A	chr2:96806742-96812863	Raji	blood:	n/a	n/a
26	EP300	chr2:96810859-96812900	GM12878	blood:	n/a	chr2:96812145-96812161 chr2:96812146-96812162 chr2:96811182-96811198
27	RFX5	chr2:96810682-96811456	GM12878	blood:	n/a	n/a
28	SRF	chr2:96810770-96811539	ECC-1	luminal epithelium:	n/a	chr2:96811229-96811247 chr2:96811230-96811247 chr2:96811232-96811245 chr2:96811233-96811247 chr2:96811231-96811246
29	NRF1	chr2:96810914-96812492	GM12878	blood:	n/a	n/a
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	EGR1	chr2:96810998-96811569	MCF-7	breast:	n/a	chr2:96811449-96811459
33	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
34	POLR2A	chr2:96806166-96813187	GM19193	blood:	n/a	n/a
35	POLR2A	chr2:96805990-96812814	GM12892	blood:	n/a	n/a
36	EGR1	chr2:96811072-96811527	ECC-1	luminal epithelium:	n/a	chr2:96811449-96811459
37	POU2F2	chr2:96807432-96811594	GM12878	blood:	n/a	n/a
38	NFATC1	chr2:96806082-96812882	GM12878	blood:	n/a	n/a
39	TAF1	chr2:96810787-96811481	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:96807735-96811533	NB4	blood:	n/a	n/a
41	PML	chr2:96810775-96811582	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:96797189-96814534	GM12892	blood:	n/a	n/a
43	BRCA1	chr2:96807827-96811711	GM12878	blood:	n/a	n/a
44	MXI1	chr2:96810057-96811616	IMR90	lung:	n/a	n/a
45	MTA3	chr2:96806625-96815107	GM12878	blood:	n/a	n/a
46	RELA	chr2:96810821-96812597	GM12892	blood:	n/a	chr2:96811972-96811981 chr2:96811972-96811981
47	MAX	chr2:96809734-96811537	MCF-7	breast:	n/a	chr2:96811287-96811296
48	SMARCB1	chr2:96809096-96813054	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr2:96807671-96812790	GM18526	blood:	n/a	n/a
50	SIN3A	chr2:96807978-96812336	GM12878	blood:	n/a	chr2:96811156-96811169

No.	Distal block	Cell Line	Cell type
1	chr17:41322227..41323055-chr2:96810694..96811756,3	Hela-S3	cervix:
2	chr2:96781378..96786213-chr2:96808688..96812498,6	MCF-7	breast:
3	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
4	chr19:5622641..5623448-chr2:96810760..96811546,2	Hela-S3	cervix:
5	chr2:96808739..96811929-chr2:96872960..96875920,3	MCF-7	breast:
6	chr2:96781942..96784647-chr2:96809826..96814461,4	MCF-7	breast:
7	chr1:109968650..109969434-chr2:96811037..96811595,2	Hela-S3	cervix:
8	chr13:21347363..21348331-chr2:96810707..96811560,2	NB4	blood:
9	chr2:96810724..96811482-chr6:31782507..31783438,2	Hela-S3	cervix:
10	chr1:159894777..159895363-chr2:96811141..96811936,2	Hela-S3	cervix:
11	chr11:45168231..45168959-chr2:96810761..96811512,2	Hela-S3	cervix:
12	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:
13	chr2:96810729..96811638-chr3:27525534..27526283,2	Hela-S3	cervix:
14	chr11:57078335..57079106-chr2:96810799..96811698,2	Hela-S3	cervix:

Variant related genes	Relation type
DUSP2	TF binding region
ENSG00000204685	Chromatin interaction
ENSG00000188554	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000143106	Chromatin interaction
ENSG00000160633	Chromatin interaction
ENSG00000033867	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000150456	Chromatin interaction
ENSG00000149115	Chromatin interaction
ENSG00000222040	Chromatin interaction
ENSG00000019485	Chromatin interaction
ENSG00000204390	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000130254	Chromatin interaction
ENSG00000267002	Chromatin interaction
ENSG00000204389	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1724120	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2969489	ADRA2B	cis	cerebellum	SCAN
rs2969489	KIAA1310	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96808800-96811800	Weak transcription	K562	blood
2	chr2:96809200-96811600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:96809600-96812200	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:96809600-96813000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:96809800-96811600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:96809800-96811600	Flanking Active TSS	HMEC	breast
7	chr2:96809800-96812400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:96809800-96812600	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr2:96810000-96811600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr2:96810000-96811600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:96810000-96811600	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr2:96810000-96812600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr2:96810000-96815000	Enhancers	Fetal Heart	heart
14	chr2:96810200-96811600	Active TSS	HSMM	muscle
15	chr2:96810200-96812600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:96810400-96811600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:96810400-96811600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:96810400-96811800	Flanking Active TSS	Colonic Mucosa	Colon
19	chr2:96810400-96811800	Bivalent Enhancer	Fetal Brain Male	brain
20	chr2:96810400-96811800	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr2:96810400-96812400	Active TSS	Thymus	Thymus
22	chr2:96810400-96813000	Flanking Active TSS	Dnd41	blood
23	chr2:96810400-96815000	Enhancers	Fetal Lung	lung
24	chr2:96810600-96811600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:96810600-96811600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:96810600-96811600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:96810600-96811600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr2:96810600-96811600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr2:96810600-96812800	Enhancers	Stomach Mucosa	stomach
30	chr2:96810800-96811600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:96811000-96811600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr2:96811000-96811600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:96811200-96811600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:96811200-96811600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:96811200-96811600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr2:96811200-96811600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:96811200-96811600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
38	chr2:96811200-96811600	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr2:96811200-96811600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
40	chr2:96811200-96811600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:96811200-96811600	Enhancers	NHDF-Ad	bronchial
42	chr2:96811200-96811800	Weak transcription	Brain Angular Gyrus	brain
43	chr2:96811200-96812200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:96811200-96812200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:96811200-96812400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr2:96811200-96812600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
47	chr2:96811200-96812800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr2:96811200-96812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:96811200-96812800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr2:96811200-96814000	Weak transcription	HUVEC	blood vessel

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