Variant report

Variant	rs28369925
Chromosome Location	chr2:100107487-100107488
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	SMC3	chr2:100105508-100107588	SK-N-SH	brain:	n/a	chr2:100106781-100106791 chr2:100107022-100107036
2	CTCF	chr2:100107340-100107490	HCM	heart:	n/a	n/a
3	RAD21	chr2:100106289-100107576	SK-N-SH	brain:	n/a	chr2:100106745-100106757 chr2:100107026-100107038 chr2:100107018-100107037 chr2:100107028-100107035
4	CTCF	chr2:100106580-100107494	HCT-116	colon:	n/a	chr2:100107020-100107038 chr2:100106698-100106711 chr2:100107015-100107036 chr2:100107021-100107037
5	HCFC1	chr2:100104811-100107753	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr2:100107397-100107824	H1-hESC	embryonic stem cell:	n/a	chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107727-100107738 chr2:100107727-100107740
7	RFX5	chr2:100106545-100107641	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr2:100105858-100107896	Hela-S3	cervix:	n/a	chr2:100107729-100107738 chr2:100107729-100107738 chr2:100106054-100106067 chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107727-100107738 chr2:100107727-100107740
9	TBL1XR1	chr2:100106020-100107536	K562	blood:	n/a	n/a
10	CTCF	chr2:100105078-100107548	SK-N-SH	brain:	n/a	chr2:100107020-100107038 chr2:100106518-100106534 chr2:100106698-100106711 chr2:100107015-100107036 chr2:100106185-100106198 chr2:100107021-100107037
11	CEBPB	chr2:100107414-100107879	A549	lung:	n/a	chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107729-100107738 chr2:100107727-100107738 chr2:100107729-100107738 chr2:100107727-100107740
12	NRF1	chr2:100105787-100107627	SK-N-SH	brain:	n/a	chr2:100105880-100105894 chr2:100106455-100106464 chr2:100106457-100106466 chr2:100106575-100106589 chr2:100106534-100106543 chr2:100106888-100106902
13	CEBPB	chr2:100106712-100107908	IMR90	lung:	n/a	chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107727-100107738 chr2:100107727-100107740
14	JUN	chr2:100105186-100107778	K562	blood:	n/a	n/a
15	MYC	chr2:100105250-100107584	NB4	blood:	n/a	chr2:100106711-100106727 chr2:100106719-100106730 chr2:100106720-100106729
16	RFX5	chr2:100106719-100107615	K562	blood:	n/a	n/a
17	RCOR1	chr2:100105710-100107554	HepG2	liver:	n/a	n/a
18	MAZ	chr2:100104810-100107714	IMR90	lung:	n/a	chr2:100106711-100106727 chr2:100106719-100106730 chr2:100106720-100106729
19	CTCF	chr2:100106211-100107822	A549	lung:	n/a	chr2:100107020-100107038 chr2:100106518-100106534 chr2:100106698-100106711 chr2:100107015-100107036 chr2:100107021-100107037
20	CTCF	chr2:100107380-100107530	NHDF-neo	bronchial:	n/a	n/a
21	CTCF	chr2:100107460-100107610	HPAF	blood vessel:	n/a	n/a
22	CEBPB	chr2:100106813-100107879	K562	blood:	n/a	chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107727-100107738 chr2:100107727-100107740
23	CTCF	chr2:100106323-100107493	GM12878	blood:	n/a	chr2:100107020-100107038 chr2:100106518-100106534 chr2:100106698-100106711 chr2:100107015-100107036 chr2:100107021-100107037
24	MYC	chr2:100105626-100107555	K562	blood:	n/a	chr2:100106711-100106727 chr2:100106719-100106730 chr2:100106720-100106729
25	CEBPB	chr2:100106677-100107907	HepG2	liver:	n/a	chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107729-100107738 chr2:100107727-100107740 chr2:100107727-100107738 chr2:100107727-100107740

No.	Distal block	Cell Line	Cell type
1	chr2:99950963..99955972-chr2:100104881..100108306,7	MCF-7	breast:
2	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
3	chr2:100075556..100080404-chr2:100103648..100108163,7	K562	blood:
4	chr2:99950324..99955285-chr2:100104603..100108030,8	MCF-7	breast:
5	chr2:99951055..99957153-chr2:100104418..100108530,14	K562	blood:
6	chr2:99796217..99798600-chr2:100104908..100107681,3	K562	blood:
7	chr2:100059011..100059845-chr2:100106953..100107584,3	MCF-7	breast:
8	chr2:100019781..100021613-chr2:100105810..100107711,2	MCF-7	breast:
9	chr2:99796217..99799127-chr2:100105224..100108883,4	K562	blood:
10	chr2:99951256..99955616-chr2:100104663..100107649,9	K562	blood:
11	chr2:100019850..100022413-chr2:100104870..100107869,3	MCF-7	breast:

Variant related genes	Relation type
REV1	TF binding region
ENSG00000135945	Chromatin interaction
ENSG00000273306	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11123785	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12053566	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12233086	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12233126	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1451245	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242036	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28369944	0.80[EUR][1000 genomes]
rs28382892	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28382949	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3791213	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3792135	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792136	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57043099	0.90[AMR][1000 genomes]
rs58766196	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59360884	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60572342	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60730619	0.80[EUR][1000 genomes]
rs61577246	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727483	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6728175	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72956308	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72956312	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72956317	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72956346	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72956387	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72958366	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72958380	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9941566	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806302	chr2:100094799-100123030	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1809009	chr2:100103752-100109251	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv582524	chr2:100103752-100110353	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3354592	chr2:100104020-100108718	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100104800-100107600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:100105000-100107600	Active TSS	A549	lung
3	chr2:100105000-100107600	Active TSS	HSMMtube	muscle
4	chr2:100105400-100107600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:100106800-100107600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:100106800-100107600	Active TSS	Fetal Brain Male	brain
7	chr2:100106800-100107600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr2:100106800-100107600	Flanking Active TSS	Thymus	Thymus
9	chr2:100107000-100107600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:100107000-100107600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:100107000-100107600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr2:100107000-100107600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:100107000-100107600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:100107000-100107600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr2:100107000-100107600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr2:100107000-100107600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr2:100107000-100107600	Flanking Active TSS	Liver	Liver
18	chr2:100107000-100107600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr2:100107000-100107600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr2:100107000-100107600	Flanking Active TSS	Fetal Brain Female	brain
21	chr2:100107000-100107600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr2:100107000-100107600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr2:100107000-100107600	Flanking Active TSS	Dnd41	blood
24	chr2:100107000-100107600	Flanking Active TSS	GM12878-XiMat	blood
25	chr2:100107000-100107600	Flanking Active TSS	HMEC	breast
26	chr2:100107000-100107600	Flanking Active TSS	NHEK	skin
27	chr2:100107000-100107600	Flanking Active TSS	NHLF	lung
28	chr2:100107200-100107600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:100107200-100107600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:100107200-100107600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:100107200-100107600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:100107200-100107600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr2:100107200-100107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:100107200-100107600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:100107200-100107600	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr2:100107200-100107600	Enhancers	Colon Smooth Muscle	Colon
37	chr2:100107200-100107600	Enhancers	Fetal Heart	heart
38	chr2:100107200-100107600	Enhancers	Fetal Lung	lung
39	chr2:100107200-100107600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr2:100107200-100107600	Flanking Active TSS	K562	blood
41	chr2:100107400-100107600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:100107400-100107600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:100107400-100107600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:100107400-100107600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:100107400-100107600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:100107400-100107600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:100107400-100107600	Enhancers	Primary B cells from peripheral blood	blood
48	chr2:100107400-100107600	Enhancers	Primary T cells from cord blood	blood
49	chr2:100107400-100107600	Enhancers	Primary hematopoietic stem cells	blood
50	chr2:100107400-100107600	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links