Variant report

Variant	rs3852537
Chromosome Location	chr12:123361501-123361502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123359999..123363082-chr12:123363364..123366412,4	MCF-7	breast:
2	chr12:123356440..123358585-chr12:123360097..123361963,2	K562	blood:
3	chr12:123356727..123361663-chr12:123362714..123365634,4	K562	blood:
4	chr12:123358138..123360225-chr12:123360853..123363329,2	MCF-7	breast:
5	chr12:123336928..123338440-chr12:123360381..123363029,2	K562	blood:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10744422	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10744434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773627	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10773657	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10847826	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10847869	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11060064	0.81[CHB][hapmap]
rs11060065	0.81[CHB][hapmap]
rs12255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12298151	0.83[ASN][1000 genomes]
rs12313006	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs12314544	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs12426809	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1532835	0.91[EUR][1000 genomes]
rs1587856	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1696326	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1799618	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2061098	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2061101	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs2271049	0.83[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs2271051	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2292132	0.89[EUR][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs2292135	0.91[EUR][1000 genomes]
rs2292136	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2292138	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292139	0.85[ASN][1000 genomes]
rs2343108	0.90[EUR][1000 genomes]
rs2343109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2343685	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2880678	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817094	0.89[EUR][1000 genomes]
rs3825143	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3852536	0.91[EUR][1000 genomes]
rs4759355	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759381	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4759382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4759386	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4759387	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4759392	0.81[AMR][1000 genomes]
rs4759393	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs59192320	0.85[ASN][1000 genomes]
rs6489245	1.00[CEU][hapmap]
rs6489247	0.83[CEU][hapmap]
rs7138398	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7139055	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7294991	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs7957643	0.82[CEU][hapmap]
rs7959441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972447	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7980541	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs839360	0.86[CHB][hapmap]
rs897385	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897391	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs897392	0.83[AMR][1000 genomes]
rs897393	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs921808	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs936083	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937766	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers 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	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123355800-123363600	Weak transcription	Dnd41	blood
2	chr12:123356200-123361800	Enhancers	Fetal Heart	heart
3	chr12:123356200-123368600	Weak transcription	Hela-S3	cervix
4	chr12:123356400-123362400	Enhancers	Liver	Liver
5	chr12:123356600-123364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:123356800-123361800	Enhancers	Fetal Thymus	thymus
7	chr12:123356800-123362200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:123356800-123363600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:123356800-123369200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:123356800-123370000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:123357000-123361600	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:123357000-123362400	Enhancers	Brain Hippocampus Middle	brain
13	chr12:123357000-123362800	Enhancers	Fetal Muscle Trunk	muscle
14	chr12:123357000-123365600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:123357000-123369800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:123357000-123373000	Weak transcription	Aorta	Aorta
17	chr12:123357200-123362000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:123357200-123362200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:123357200-123362400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:123357200-123363800	Weak transcription	K562	blood
21	chr12:123357200-123365200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:123357800-123362800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:123358200-123367200	Weak transcription	HUVEC	blood vessel
24	chr12:123358600-123361600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:123358600-123363400	Weak transcription	Esophagus	oesophagus
26	chr12:123358800-123362000	Weak transcription	Fetal Stomach	stomach
27	chr12:123358800-123371400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:123359000-123361600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:123359000-123362000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:123359000-123365000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:123359000-123365200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:123359000-123368400	Weak transcription	Fetal Intestine Large	intestine
33	chr12:123359000-123369600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr12:123359400-123361800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:123359400-123366000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:123359600-123361600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr12:123359600-123361800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:123359600-123362200	Enhancers	Fetal Muscle Leg	muscle
39	chr12:123359600-123365000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr12:123359600-123366200	Enhancers	Right Atrium	heart
41	chr12:123359800-123361600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:123359800-123362200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:123359800-123362400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:123360000-123361800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:123360000-123362000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:123360000-123362400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:123360000-123362400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:123360000-123362400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:123360000-123362600	Enhancers	Adipose Nuclei	Adipose
50	chr12:123360200-123362000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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