Variant report

Variant	rs58446419
Chromosome Location	chr2:97539830-97539831
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	UBTF	chr2:97539367-97540290	K562	blood:	n/a	n/a
2	CHD2	chr2:97539396-97540712	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:97539812-97540887	GM12892	blood:	n/a	n/a
4	EBF1	chr2:97539409-97540780	GM12878	blood:	n/a	chr2:97539963-97539973 chr2:97539962-97539973 chr2:97539963-97539972
5	POLR2A	chr2:97539653-97541196	GM12892	blood:	n/a	n/a
6	ZMIZ1	chr2:97539267-97539857	K562	blood:	n/a	n/a
7	REST	chr2:97539399-97539860	K562	blood:	n/a	n/a
8	EBF1	chr2:97539225-97540757	GM12878	blood:	n/a	chr2:97539963-97539973 chr2:97539962-97539973 chr2:97539963-97539972
9	PML	chr2:97539786-97540709	GM12878	blood:	n/a	n/a
10	RELA	chr2:97539442-97540710	GM19099	blood:	n/a	n/a
11	POLR2A	chr2:97539243-97541503	GM12878	blood:	n/a	n/a
12	SMC3	chr2:97539363-97540556	GM12878	blood:	n/a	n/a
13	MAFK	chr2:97539312-97540184	K562	blood:	n/a	chr2:97539623-97539638
14	POLR2A	chr2:97539277-97543077	K562	blood:	n/a	n/a
15	POLR2A	chr2:97537838-97552897	K562	blood:	n/a	n/a
16	PML	chr2:97539335-97539841	K562	blood:	n/a	n/a
17	POLR2A	chr2:97539500-97541285	GM12878	blood:	n/a	n/a
18	RELA	chr2:97539775-97540653	GM18505	blood:	n/a	n/a
19	ELF1	chr2:97539294-97540740	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:97538088-97552551	K562	blood:	n/a	n/a
21	TEAD4	chr2:97539371-97540057	K562	blood:	n/a	n/a
22	POLR2A	chr2:97538469-97541757	MCF10A-Er-Src	breast:	n/a	n/a
23	RUNX3	chr2:97539337-97539995	GM12878	blood:	n/a	n/a
24	RCOR1	chr2:97539313-97540546	K562	blood:	n/a	n/a
25	RFX5	chr2:97539320-97540075	GM12878	blood:	n/a	n/a
26	IKZF1	chr2:97539406-97539878	GM12878	blood:	n/a	n/a
27	RCOR1	chr2:97539442-97540826	GM12878	blood:	n/a	n/a
28	EP300	chr2:97539381-97540828	GM12878	blood:	n/a	chr2:97539547-97539561 chr2:97540264-97540273
29	POLR2A	chr2:97539817-97540757	GM19193	blood:	n/a	n/a
30	NR2F2	chr2:97539711-97540148	K562	blood:	n/a	n/a
31	POLR2A	chr2:97538464-97546326	K562	blood:	n/a	n/a
32	RELA	chr2:97539603-97540817	GM12891	blood:	n/a	n/a
33	POLR2A	chr2:97539214-97541233	GM12878	blood:	n/a	n/a
34	MTA3	chr2:97539280-97541275	GM12878	blood:	n/a	n/a
35	WRNIP1	chr2:97539500-97540767	GM12878	blood:	n/a	n/a
36	JUND	chr2:97538762-97540098	K562	blood:	n/a	n/a
37	EBF1	chr2:97539747-97540825	GM12878	blood:	n/a	chr2:97539963-97539973 chr2:97539962-97539973 chr2:97539963-97539972
38	MAZ	chr2:97538723-97540459	K562	blood:	n/a	n/a
39	POLR2A	chr2:97538440-97541798	K562	blood:	n/a	n/a
40	TBP	chr2:97539381-97540806	GM12878	blood:	n/a	n/a
41	USF2	chr2:97539562-97540666	GM12878	blood:	n/a	n/a
42	TBL1XR1	chr2:97539429-97539847	K562	blood:	n/a	n/a
43	POLR2A	chr2:97538536-97540297	K562	blood:	n/a	n/a
44	RELA	chr2:97539453-97540841	GM12878	blood:	n/a	n/a
45	SPI1	chr2:97539053-97540749	GM12878	blood:	n/a	chr2:97540264-97540273 chr2:97539552-97539561 chr2:97539548-97539557 chr2:97540265-97540272 chr2:97540263-97540276 chr2:97539546-97539559 chr2:97540262-97540275
46	POLR2A	chr2:97538291-97540512	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
2	chr2:97538315..97540363-chr2:97559572..97561946,2	K562	blood:
3	chr2:97539206..97539881-chr2:97616937..97617560,2	MCF-7	breast:
4	chr2:97536575..97540877-chr2:97558007..97561072,4	K562	blood:
5	chr2:97539206..97540823-chr2:97583681..97585433,2	K562	blood:
6	chr2:97538577..97540759-chr2:97582330..97584381,2	K562	blood:

Variant related genes	Relation type
SEMA4C	TF binding region
ENSG00000168754	Chromatin interaction
ENSG00000252845	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11885652	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473528	0.80[EUR][1000 genomes]
rs59271006	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62152867	0.94[EUR][1000 genomes]
rs6750988	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6758174	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7581764	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536600-97541600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr2:97536800-97542000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:97536800-97546200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:97536800-97551800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:97537000-97540200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:97537000-97540200	Weak transcription	Fetal Lung	lung
8	chr2:97537000-97540800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:97537000-97540800	Weak transcription	Fetal Brain Male	brain
10	chr2:97537000-97541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:97537000-97542200	Enhancers	Placenta	Placenta
12	chr2:97537200-97540000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:97537200-97540600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:97537200-97540800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:97537200-97540800	Weak transcription	Fetal Brain Female	brain
16	chr2:97537400-97540000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:97537400-97540600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:97537400-97540800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:97537800-97544200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:97538000-97540000	Enhancers	Right Atrium	heart
21	chr2:97538000-97541000	Enhancers	Right Ventricle	heart
22	chr2:97538000-97543800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:97538400-97540000	Enhancers	GM12878-XiMat	blood
24	chr2:97538400-97540000	Enhancers	NHEK	skin
25	chr2:97538400-97540000	Enhancers	Osteobl	bone
26	chr2:97538400-97540200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:97538400-97540200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:97538400-97540200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:97538400-97540600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:97538400-97540600	Enhancers	HMEC	breast
31	chr2:97538400-97540800	Enhancers	Left Ventricle	heart
32	chr2:97538400-97541800	Enhancers	Fetal Kidney	kidney
33	chr2:97538400-97542400	Enhancers	Brain Substantia Nigra	brain
34	chr2:97538400-97544400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr2:97538400-97547400	Enhancers	Spleen	Spleen
36	chr2:97538600-97540000	Enhancers	Fetal Heart	heart
37	chr2:97538600-97540200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:97538600-97540400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr2:97538600-97540400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:97538600-97540600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:97538600-97540600	Enhancers	Pancreas	Pancrea
42	chr2:97538600-97540800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:97538600-97541000	Enhancers	Adipose Nuclei	Adipose
44	chr2:97538600-97541200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:97538600-97541200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:97538600-97541200	Enhancers	Esophagus	oesophagus
47	chr2:97538600-97541800	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:97538600-97542000	Enhancers	Fetal Muscle Leg	muscle
49	chr2:97538600-97542400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:97538600-97542600	Enhancers	Fetal Stomach	stomach

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