Variant report

Variant	rs2566972
Chromosome Location	chr3:113460429-113460430
allele	C/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	POLR2A	chr3:113460321-113460448	MCF10A-Er-Src	breast:	n/a	n/a
2	CUX1	chr3:113460290-113460455	GM12878	blood:	n/a	n/a
3	NFATC1	chr3:113460033-113460842	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:113460426-113460530	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:113459236-113460535	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113446389..113448744-chr3:113460287..113462376,2	K562	blood:
2	chr3:113435155..113437816-chr3:113460130..113462282,2	K562	blood:

Variant related genes	Relation type
ENSG00000239280	TF binding region
NAA50	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934239	0.85[MEX][hapmap]
rs11921407	0.85[MEX][hapmap]
rs12486414	0.85[MEX][hapmap];0.87[AMR][1000 genomes]
rs12489192	0.87[AMR][1000 genomes]
rs12490048	0.81[AMR][1000 genomes]
rs12490651	0.87[AMR][1000 genomes]
rs12491540	0.87[AMR][1000 genomes]
rs12492290	0.87[AMR][1000 genomes]
rs12492542	0.85[MEX][hapmap];0.87[AMR][1000 genomes]
rs12492783	0.81[AMR][1000 genomes]
rs12493602	0.85[MEX][hapmap];0.87[AMR][1000 genomes]
rs12494777	0.87[AMR][1000 genomes]
rs12495298	0.93[AMR][1000 genomes]
rs12495713	0.87[AMR][1000 genomes]
rs12496604	0.87[AMR][1000 genomes]
rs12496617	0.81[AMR][1000 genomes]
rs12497754	0.87[AMR][1000 genomes]
rs16861230	0.81[AMR][1000 genomes]
rs16861233	0.81[AMR][1000 genomes]
rs16861235	0.81[AMR][1000 genomes]
rs16861331	0.87[AMR][1000 genomes]
rs2290477	0.85[GIH][hapmap]
rs2292512	0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs2603791	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3773686	0.81[AMR][1000 genomes]
rs3821678	1.00[JPT][hapmap]

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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv1799124	chr3:113426201-113468350	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113432800-113463000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:113432800-113463000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:113435000-113463000	Weak transcription	Brain Germinal Matrix	brain
4	chr3:113435200-113463000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:113435200-113463000	Weak transcription	Esophagus	oesophagus
6	chr3:113435400-113462600	Weak transcription	Brain Angular Gyrus	brain
7	chr3:113435600-113462200	Weak transcription	Thymus	Thymus
8	chr3:113436000-113462800	Weak transcription	Spleen	Spleen
9	chr3:113437200-113464000	Weak transcription	Lung	lung
10	chr3:113440800-113461200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:113440800-113461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:113440800-113463000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:113440800-113463600	Weak transcription	Ovary	ovary
14	chr3:113441400-113462800	Weak transcription	Fetal Brain Male	brain
15	chr3:113442200-113462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:113442200-113463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:113442400-113462200	Weak transcription	NH-A	brain
18	chr3:113443000-113461000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:113446000-113463000	Weak transcription	Left Ventricle	heart
20	chr3:113449200-113462800	Weak transcription	Fetal Intestine Small	intestine
21	chr3:113449800-113461800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:113451000-113462600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:113451600-113461000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:113451600-113462800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:113453600-113463600	Enhancers	Liver	Liver
26	chr3:113455000-113460600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:113455200-113463200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:113455800-113462400	Weak transcription	Fetal Kidney	kidney
29	chr3:113455800-113462600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:113455800-113462800	Weak transcription	Fetal Stomach	stomach
31	chr3:113456000-113461400	Weak transcription	Fetal Intestine Large	intestine
32	chr3:113456000-113461800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:113456000-113462800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:113456200-113462000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:113456200-113462200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:113456200-113462400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:113456200-113462600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:113456600-113462600	Weak transcription	Stomach Mucosa	stomach
39	chr3:113456800-113461800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:113456800-113463000	Weak transcription	Right Ventricle	heart
41	chr3:113456800-113463600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:113457000-113463000	Weak transcription	Pancreas	Pancrea
43	chr3:113457200-113461400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:113457200-113462200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:113458000-113462200	Weak transcription	Fetal Brain Female	brain
46	chr3:113458000-113462400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:113458200-113462600	Weak transcription	Brain Substantia Nigra	brain
48	chr3:113458600-113461600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:113458600-113461800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:113458600-113462000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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