Variant report

Variant	rs57240461
Chromosome Location	chr12:51840403-51840404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51835581..51837352-chr12:51839270..51841955,2	MCF-7	breast:
2	chr12:51839420..51841237-chr12:51848680..51850219,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17125750	1.00[AMR][1000 genomes]
rs17125765	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125848	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59873570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs767336	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs873674	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1038285	chr12:51762953-51916723	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1045796	chr12:51794043-51844027	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv519438	chr12:51837789-51900105	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51819000-51860800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:51820600-51842000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:51820600-51844400	Weak transcription	Brain Germinal Matrix	brain
4	chr12:51827000-51851000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:51827400-51866800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:51829200-51840600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:51831600-51847200	Weak transcription	Dnd41	blood
8	chr12:51833000-51842400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:51833800-51845800	Weak transcription	Primary T cells from cord blood	blood
10	chr12:51834200-51841400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:51834200-51842000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:51834200-51842200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:51834600-51842000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:51835800-51868800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:51836000-51840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:51836200-51868600	Weak transcription	NHLF	lung
17	chr12:51836600-51846200	Weak transcription	Fetal Brain Female	brain
18	chr12:51836600-51850600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:51836600-51851800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:51836600-51854200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:51836800-51840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:51836800-51842400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:51836800-51845600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:51836800-51846000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:51836800-51846000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:51836800-51847200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:51837000-51845800	Weak transcription	Brain Anterior Caudate	brain
28	chr12:51837000-51846000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:51837200-51841200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:51839200-51876200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:51839600-51849000	Weak transcription	Fetal Intestine Small	intestine
32	chr12:51840200-51840600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:51840200-51840600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:51840200-51840600	Enhancers	Brain Hippocampus Middle	brain
35	chr12:51840200-51840600	Enhancers	Stomach Mucosa	stomach
36	chr12:51840200-51867200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links