Variant report

Variant	rs73924013
Chromosome Location	chr2:39661090-39661091
allele	C/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	EP300	chr2:39660983-39661151	GM12878	blood:	n/a	n/a
2	GATA2	chr2:39660713-39661113	K562	blood:	n/a	chr2:39660959-39660968 chr2:39660907-39660917
3	ARID3A	chr2:39660791-39661256	K562	blood:	n/a	n/a
4	GATA1	chr2:39660629-39661905	PBDE	blood:	n/a	chr2:39660959-39660968 chr2:39660907-39660917 chr2:39661770-39661783 chr2:39661593-39661600
5	TBL1XR1	chr2:39660779-39661101	K562	blood:	n/a	n/a
6	RCOR1	chr2:39660814-39661177	K562	blood:	n/a	n/a
7	CEBPB	chr2:39660861-39661184	K562	blood:	n/a	n/a
8	TBL1XR1	chr2:39660629-39661229	K562	blood:	n/a	n/a
9	EP300	chr2:39660623-39661109	K562	blood:	n/a	n/a
10	JUND	chr2:39660792-39661150	K562	blood:	n/a	chr2:39661024-39661032 chr2:39661025-39661032
11	CEBPD	chr2:39660731-39661121	K562	blood:	n/a	n/a
12	UBTF	chr2:39660714-39661200	K562	blood:	n/a	n/a
13	TAL1	chr2:39660716-39661126	K562	blood:	n/a	n/a
14	CTCF	chr2:39661020-39661170	AG09319	gingival:	n/a	n/a
15	TEAD4	chr2:39660742-39661130	K562	blood:	n/a	n/a
16	CTCF	chr2:39660980-39661130	HCFaa	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39652432..39656926-chr2:39657241..39661273,4	MCF-7	breast:
2	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
3	chr2:39654384..39656809-chr2:39659803..39661309,2	MCF-7	breast:
4	chr2:39655304..39658022-chr2:39658367..39662517,3	K562	blood:

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11886110	0.81[AFR][1000 genomes]
rs11886434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895366	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11902188	0.82[AFR][1000 genomes]
rs55750780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55961227	0.84[AFR][1000 genomes]
rs56928728	0.81[AFR][1000 genomes]
rs57084694	0.98[AFR][1000 genomes]
rs58824151	0.84[AFR][1000 genomes]
rs59896787	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60394429	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544225	0.84[AFR][1000 genomes]
rs6712399	0.85[AFR][1000 genomes]
rs6723987	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727395	0.85[AFR][1000 genomes]
rs6751506	0.85[AFR][1000 genomes]
rs73923887	0.84[AFR][1000 genomes]
rs73923888	0.84[AFR][1000 genomes]
rs73923889	0.84[AFR][1000 genomes]
rs73923895	0.82[AFR][1000 genomes]
rs73924011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7565210	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591563	0.84[AFR][1000 genomes]
rs7599017	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:39652000-39662400	Weak transcription	Esophagus	oesophagus
3	chr2:39652000-39662400	Weak transcription	Lung	lung
4	chr2:39652400-39661200	Weak transcription	HUVEC	blood vessel
5	chr2:39652800-39661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:39652800-39661400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:39652800-39661600	Weak transcription	Fetal Thymus	thymus
8	chr2:39656600-39661200	Enhancers	Fetal Heart	heart
9	chr2:39656600-39661800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:39656600-39662200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:39657200-39661200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:39657400-39661600	Enhancers	Adipose Nuclei	Adipose
13	chr2:39657600-39661200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:39657800-39661600	Enhancers	NHDF-Ad	bronchial
15	chr2:39657800-39661800	Enhancers	Colon Smooth Muscle	Colon
16	chr2:39657800-39662400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:39658000-39661400	Enhancers	HSMMtube	muscle
18	chr2:39658000-39661600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:39658000-39661600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:39658000-39662400	Enhancers	Liver	Liver
21	chr2:39658200-39661200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:39658200-39661600	Enhancers	Hela-S3	cervix
23	chr2:39658200-39662400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:39658400-39661800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:39658400-39662400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:39658600-39662800	Enhancers	Stomach Mucosa	stomach
27	chr2:39658600-39663000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr2:39659000-39661600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr2:39659000-39663000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:39659200-39661800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:39659200-39661800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:39659200-39661800	Enhancers	Brain Substantia Nigra	brain
33	chr2:39659200-39662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:39659200-39662600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:39659200-39663400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:39659400-39661400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:39659400-39661400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:39659400-39661400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:39659400-39661400	Flanking Active TSS	HepG2	liver
40	chr2:39659400-39661600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:39659400-39661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:39659400-39662400	Active TSS	GM12878-XiMat	blood
43	chr2:39659600-39661600	Enhancers	Dnd41	blood
44	chr2:39659800-39661200	Weak transcription	Brain Anterior Caudate	brain
45	chr2:39659800-39662200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:39660000-39661400	Enhancers	Osteobl	bone
47	chr2:39660000-39661600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:39660000-39661600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:39660000-39661800	Enhancers	Psoas Muscle	Psoas
50	chr2:39660000-39662200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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