Variant report

Variant	rs12578858
Chromosome Location	chr12:51762834-51762835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51761603..51763662-chr12:51775969..51778368,2	MCF-7	breast:
2	chr12:51754295..51757629-chr12:51759740..51762921,4	K562	blood:
3	chr12:51762201..51772634-chr12:51780037..51787148,16	MCF-7	breast:
4	chr12:51761344..51767144-chr12:51781671..51788039,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139629	Chromatin interaction
ENSG00000050438	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10783438	1.00[EUR][1000 genomes]
rs12579126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580621	1.00[EUR][1000 genomes]
rs12581208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582216	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860267	1.00[EUR][1000 genomes]
rs17860283	1.00[EUR][1000 genomes]
rs17860320	1.00[EUR][1000 genomes]
rs17860337	1.00[EUR][1000 genomes]
rs2067764	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741700	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3889974	1.00[EUR][1000 genomes]
rs58448629	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60044798	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61612083	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73309782	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73309783	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73309787	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73309789	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73309790	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73309797	0.97[ASN][1000 genomes]
rs73311613	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:51745800-51763000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:51751200-51783400	Weak transcription	Right Atrium	heart
4	chr12:51752000-51765000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:51752800-51765000	Weak transcription	Placenta	Placenta
6	chr12:51752800-51765200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:51753200-51781400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:51754200-51764600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:51754400-51764600	Weak transcription	NHDF-Ad	bronchial
10	chr12:51754600-51763000	Weak transcription	Gastric	stomach
11	chr12:51755000-51765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:51755600-51765000	Weak transcription	Esophagus	oesophagus
13	chr12:51756600-51765000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:51757200-51765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:51757800-51763600	Strong transcription	Fetal Stomach	stomach
16	chr12:51757800-51764200	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr12:51757800-51765200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:51758000-51765400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:51758000-51765600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:51758200-51764400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:51758200-51765200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:51759600-51764400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:51759800-51765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:51760800-51763000	Enhancers	Primary B cells from cord blood	blood
25	chr12:51760800-51763000	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:51761200-51763000	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:51761200-51763000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:51761200-51763000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:51761200-51763000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:51761200-51763000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:51761400-51763000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:51761400-51763000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:51761400-51763000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:51761600-51764600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:51761800-51763000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:51761800-51763000	Enhancers	Dnd41	blood
37	chr12:51761800-51765600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:51762000-51763000	Enhancers	GM12878-XiMat	blood
39	chr12:51762000-51769400	Enhancers	HUVEC	blood vessel
40	chr12:51762200-51763600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr12:51762200-51765200	Enhancers	Fetal Thymus	thymus
42	chr12:51762400-51763000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr12:51762400-51763200	Genic enhancers	Fetal Intestine Small	intestine
44	chr12:51762400-51763400	Enhancers	Fetal Muscle Trunk	muscle
45	chr12:51762400-51763400	Strong transcription	NHLF	lung
46	chr12:51762400-51763600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr12:51762400-51763600	Enhancers	Spleen	Spleen
48	chr12:51762400-51763600	Enhancers	K562	blood
49	chr12:51762400-51763800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:51762400-51763800	Enhancers	Primary monocytes fromperipheralblood	blood

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