Variant report

Variant	rs3825409
Chromosome Location	chr13:51825548-51825549
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	chr13:51820571..51823207-chr13:51824938..51826606,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11617293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475377	0.95[JPT][hapmap]
rs17837207	0.95[JPT][hapmap]
rs17837209	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs17837210	0.90[JPT][hapmap]
rs4942985	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58934553	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73194192	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73194195	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73194198	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3825409	FAM124A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51805200-51825600	Weak transcription	Aorta	Aorta
2	chr13:51816200-51836600	Weak transcription	Adipose Nuclei	Adipose
3	chr13:51816800-51836000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:51817400-51827200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:51817600-51827200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:51817800-51827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:51818800-51832800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr13:51820800-51833000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:51821200-51829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:51821400-51825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:51821400-51825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:51821400-51825800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:51821400-51825800	Weak transcription	Left Ventricle	heart
14	chr13:51821400-51827200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr13:51821400-51829600	Weak transcription	Right Atrium	heart
16	chr13:51821400-51833200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr13:51821400-51833800	Weak transcription	Gastric	stomach
18	chr13:51821600-51836200	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:51821600-51839000	Weak transcription	Esophagus	oesophagus
20	chr13:51821600-51845000	Weak transcription	Fetal Brain Male	brain
21	chr13:51821800-51825600	Weak transcription	Spleen	Spleen
22	chr13:51821800-51825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr13:51821800-51831400	Weak transcription	Fetal Lung	lung
24	chr13:51822200-51833200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:51822400-51825600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:51822600-51826000	Enhancers	Pancreas	Pancrea
27	chr13:51822600-51831000	Enhancers	Fetal Heart	heart
28	chr13:51823400-51825600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:51823400-51825600	Enhancers	Brain Hippocampus Middle	brain
30	chr13:51823400-51827800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr13:51824200-51825600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:51824200-51828200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr13:51824200-51844000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:51824400-51825600	Enhancers	Colon Smooth Muscle	Colon
35	chr13:51824400-51827800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr13:51824400-51836600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr13:51824600-51825600	Enhancers	Stomach Smooth Muscle	stomach
38	chr13:51824600-51826000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:51824600-51827200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:51824800-51825600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:51824800-51827000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr13:51824800-51827200	Strong transcription	Fetal Brain Female	brain
43	chr13:51824800-51828000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr13:51825000-51825600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:51825000-51826600	Strong transcription	Fetal Stomach	stomach
46	chr13:51825000-51828000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:51825000-51829000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr13:51825000-51833000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:51825200-51825800	Weak transcription	Brain Angular Gyrus	brain
50	chr13:51825200-51825800	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links