Variant report

Variant	rs2138604
Chromosome Location	chr2:113484319-113484320
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:238)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:238 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:113484250-113484647	HepG2	liver:	n/a	n/a
2	ZMIZ1	chr2:113484319-113484626	K562	blood:	n/a	n/a
3	MAZ	chr2:113484128-113485071	IMR90	lung:	n/a	chr2:113485038-113485048
4	CTCF	chr2:113484196-113484589	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr2:113484246-113484658	GM12891	blood:	n/a	n/a
6	TBL1XR1	chr2:113484116-113484616	GM12878	blood:	n/a	n/a
7	CEBPB	chr2:113484261-113484678	Hela-S3	cervix:	n/a	n/a
8	BHLHE40	chr2:113484273-113484609	K562	blood:	n/a	n/a
9	TCF12	chr2:113484305-113484686	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr2:113484293-113484646	K562	blood:	n/a	n/a
11	RFX5	chr2:113484249-113484661	Hela-S3	cervix:	n/a	n/a
12	RELA	chr2:113484240-113484647	GM15510	blood:	n/a	n/a
13	BHLHE40	chr2:113484261-113484644	HepG2	liver:	n/a	n/a
14	MAX	chr2:113484194-113484750	ECC-1	luminal epithelium:	n/a	n/a
15	CHD2	chr2:113484173-113484651	HepG2	liver:	n/a	n/a
16	TBL1XR1	chr2:113484169-113484659	K562	blood:	n/a	n/a
17	CHD2	chr2:113484306-113484594	K562	blood:	n/a	n/a
18	POLR2A	chr2:113484153-113484656	HCT-116	colon:	n/a	n/a
19	CTCF	chr2:113483515-113484999	HCT-116	colon:	n/a	chr2:113483786-113483807 chr2:113483797-113483806 chr2:113483791-113483809 chr2:113484173-113484182
20	SIN3A	chr2:113484315-113484652	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr2:113484313-113484644	GM12878	blood:	n/a	n/a
22	RAD21	chr2:113484181-113484637	K562	blood:	n/a	n/a
23	CEBPB	chr2:113484311-113484621	K562	blood:	n/a	n/a
24	RAD21	chr2:113484099-113484744	MCF-7	breast:	n/a	n/a
25	BATF	chr2:113484287-113484572	GM12878	blood:	n/a	n/a
26	ARID3A	chr2:113484256-113484623	HepG2	liver:	n/a	n/a
27	EGR1	chr2:113484184-113484538	K562	blood:	n/a	chr2:113484349-113484363
28	NFIC	chr2:113484094-113484611	HepG2	liver:	n/a	n/a
29	RAD21	chr2:113484218-113484699	HepG2	liver:	n/a	n/a
30	SPI1	chr2:113484105-113484566	GM12891	blood:	n/a	n/a
31	CTCF	chr2:113484250-113484698	K562	blood:	n/a	n/a
32	EP300	chr2:113484192-113484604	GM12878	blood:	n/a	n/a
33	SPI1	chr2:113484249-113484515	K562	blood:	n/a	n/a
34	CTCF	chr2:113484305-113484658	GM19238	blood:	n/a	n/a
35	ZNF143	chr2:113484291-113484656	H1-hESC	embryonic stem cell:	n/a	n/a
36	RELA	chr2:113484074-113484624	GM19099	blood:	n/a	n/a
37	CTCF	chr2:113484238-113484661	K562	blood:	n/a	n/a
38	CTCF	chr2:113484159-113484771	HCT-116	colon:	n/a	chr2:113484173-113484182
39	TBP	chr2:113484221-113484555	GM12878	blood:	n/a	n/a
40	EBF1	chr2:113483398-113484689	GM12878	blood:	n/a	chr2:113484031-113484044 chr2:113483616-113483627 chr2:113484223-113484232
41	RCOR1	chr2:113484092-113484656	HepG2	liver:	n/a	n/a
42	YY1	chr2:113484286-113484589	K562	blood:	n/a	n/a
43	ZNF143	chr2:113484289-113484653	K562	blood:	n/a	n/a
44	CEBPB	chr2:113484262-113484655	A549	lung:	n/a	n/a
45	EGR1	chr2:113484192-113484456	GM12878	blood:	n/a	chr2:113484349-113484363
46	RAD21	chr2:113484098-113484801	IMR90	lung:	n/a	n/a
47	YY1	chr2:113484272-113484601	SK-N-SH_RA	brain:	n/a	n/a
48	HDAC2	chr2:113484225-113484645	MCF-7	breast:	n/a	n/a
49	WRNIP1	chr2:113484305-113484552	GM12878	blood:	n/a	n/a
50	GTF2F1	chr2:113484298-113484634	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113399891..113407010-chr2:113481534..113486055,14	K562	blood:
2	chr2:113357420..113358272-chr2:113483946..113484977,12	K562	blood:
3	chr2:113338256..113339919-chr2:113484252..113486585,3	MCF-7	breast:
4	chr2:113470986..113471535-chr2:113484133..113484894,2	K562	blood:
5	chr2:113383817..113384789-chr2:113484041..113484921,7	MCF-7	breast:
6	chr2:113402591..113403420-chr2:113483970..113484957,3	K562	blood:
7	chr2:113340042..113340549-chr2:113483924..113484572,2	K562	blood:
8	chr2:113341937..113342805-chr2:113484002..113484522,2	K562	blood:
9	chr2:113401788..113407326-chr2:113480776..113487899,15	MCF-7	breast:
10	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
11	chr2:113484246..113487026-chr2:113487818..113491393,4	MCF-7	breast:
12	chr2:113401688..113406035-chr2:113480430..113485744,11	MCF-7	breast:
13	chr2:113401171..113414378-chr2:113468812..113486672,46	K562	blood:
14	chr2:113482871..113484637-chr2:113485555..113488424,2	K562	blood:
15	chr2:113415099..113418730-chr2:113484170..113487314,3	K562	blood:
16	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
17	chr2:113237844..113240182-chr2:113482913..113484469,2	MCF-7	breast:
18	chr2:113484028..113484731-chr2:113642145..113642705,2	K562	blood:
19	chr2:113383746..113384937-chr2:113484019..113484887,5	MCF-7	breast:
20	chr2:113480533..113482697-chr2:113482909..113484492,2	K562	blood:
21	chr2:113478980..113481125-chr2:113482565..113484434,2	MCF-7	breast:
22	chr2:113340774..113345524-chr2:113480391..113485957,9	MCF-7	breast:
23	chr2:113339955..113341936-chr2:113481777..113484601,3	MCF-7	breast:
24	chr2:113357362..113358295-chr2:113483923..113484596,5	MCF-7	breast:
25	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
26	chr2:113447408..113450068-chr2:113484150..113486328,2	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC4	TF binding region
ENSG00000114999	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000144136	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10209160	0.93[AFR][1000 genomes]
rs17042344	0.86[AFR][1000 genomes]
rs2138605	0.83[AFR][1000 genomes]
rs35691553	1.00[AMR][1000 genomes]
rs3783585	1.00[AMR][1000 genomes]
rs4260249	0.93[AFR][1000 genomes]
rs56770888	1.00[AMR][1000 genomes]
rs6542088	0.86[AFR][1000 genomes]
rs6705236	1.00[AMR][1000 genomes]
rs7559917	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs908550	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS 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	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3458160	chr2:113460280-113484749	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3458161	chr2:113460322-113484724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3458162	chr2:113460460-113484652	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113464200-113486400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:113477600-113487000	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr2:113478600-113488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:113479400-113485200	Enhancers	K562	blood
5	chr2:113480000-113488200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:113481200-113487600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:113481800-113484400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:113481800-113486600	Enhancers	Placenta	Placenta
9	chr2:113482200-113484400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:113482200-113484800	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:113482200-113485000	Enhancers	Hela-S3	cervix
12	chr2:113482200-113485200	Enhancers	HMEC	breast
13	chr2:113482400-113484800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:113482400-113484800	Enhancers	Fetal Intestine Large	intestine
15	chr2:113482400-113484800	Enhancers	Fetal Intestine Small	intestine
16	chr2:113482600-113484400	Enhancers	A549	lung
17	chr2:113482600-113484800	Enhancers	NHEK	skin
18	chr2:113482800-113484800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:113483000-113488200	Enhancers	Spleen	Spleen
20	chr2:113483600-113484400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:113483600-113484400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:113483600-113484400	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:113483600-113484600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:113483600-113484600	Enhancers	NH-A	brain
25	chr2:113483600-113484800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:113483600-113484800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:113483600-113484800	Enhancers	Fetal Brain Male	brain
28	chr2:113483600-113487600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:113483800-113484600	Enhancers	Colonic Mucosa	Colon
30	chr2:113483800-113484800	Enhancers	Primary B cells from cord blood	blood
31	chr2:113483800-113484800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:113483800-113488200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr2:113484000-113484400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:113484000-113484400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:113484000-113484400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr2:113484000-113484400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:113484000-113484400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:113484000-113484400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:113484000-113484400	Enhancers	Adipose Nuclei	Adipose
40	chr2:113484000-113484400	Enhancers	Brain Anterior Caudate	brain
41	chr2:113484000-113484400	Enhancers	Brain Hippocampus Middle	brain
42	chr2:113484000-113484400	Enhancers	Brain Substantia Nigra	brain
43	chr2:113484000-113484400	Enhancers	Fetal Heart	heart
44	chr2:113484000-113484400	Enhancers	Fetal Muscle Trunk	muscle
45	chr2:113484000-113484600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr2:113484000-113484600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:113484000-113484600	Enhancers	Fetal Thymus	thymus
48	chr2:113484000-113484600	Flanking Active TSS	HepG2	liver
49	chr2:113484000-113484800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:113484000-113484800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links