Variant report

Variant	rs12489539
Chromosome Location	chr3:52121297-52121298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52119415..52123026-chr3:52140546..52143765,3	K562	blood:
2	chr3:52120428..52122434-chr3:52170670..52172571,2	K562	blood:
3	chr3:52089472..52091988-chr3:52119282..52121662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485855	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488456	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821841	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3852069	0.81[AMR][1000 genomes]
rs4687608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4687609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687798	0.81[MEX][hapmap]
rs4687801	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687802	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687808	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687809	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66530305	0.83[AMR][1000 genomes]
rs72622937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs747343	0.83[MEX][hapmap]
rs7618573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9637473	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9873175	0.86[MEX][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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active 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	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52103200-52122000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:52103200-52124800	Weak transcription	Colonic Mucosa	Colon
3	chr3:52105600-52124000	Weak transcription	Pancreas	Pancrea
4	chr3:52105800-52124000	Weak transcription	Hela-S3	cervix
5	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
6	chr3:52107200-52123200	Weak transcription	Fetal Brain Female	brain
7	chr3:52108800-52122200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52109600-52123800	Weak transcription	NHEK	skin
9	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:52110000-52121600	Weak transcription	NHLF	lung
11	chr3:52110000-52122000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:52110800-52122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:52111200-52122200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:52112400-52122200	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:52115800-52133000	Weak transcription	Gastric	stomach
25	chr3:52118800-52123200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:52118800-52124800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:52119000-52123600	Enhancers	Fetal Thymus	thymus
28	chr3:52119000-52124600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52119200-52121800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:52119200-52126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:52119200-52127200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:52119200-52128400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:52119200-52128600	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:52119600-52121600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:52119600-52123200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:52119600-52124800	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:52119600-52129000	Enhancers	Fetal Muscle Leg	muscle
38	chr3:52119800-52121400	Enhancers	Primary T cells from cord blood	blood
39	chr3:52119800-52121600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52119800-52121600	Enhancers	Thymus	Thymus
41	chr3:52119800-52121800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52119800-52122800	Enhancers	GM12878-XiMat	blood
43	chr3:52119800-52123600	Enhancers	Spleen	Spleen
44	chr3:52119800-52124200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:52120000-52125400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:52120200-52124800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr3:52120600-52121400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:52120600-52121400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:52120600-52121600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:52120600-52123000	Enhancers	Lung	lung

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