Variant report

Variant	rs17058430
Chromosome Location	chr13:39259666-39259667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr13:39258446-39259668	MCF-7	breast:	n/a	n/a
2	FOXA1	chr13:39259641-39259807	T-47D	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:39256386..39258055-chr13:39258985..39261054,2	MCF-7	breast:
2	chr13:39251483..39253844-chr13:39259100..39260979,2	MCF-7	breast:
3	chr13:39259605..39260560-chr13:39446509..39447532,4	MCF-7	breast:
4	chr13:39258919..39260831-chr13:39305195..39307479,2	MCF-7	breast:
5	chr13:39259609..39260600-chr13:39337776..39338558,4	MCF-7	breast:
6	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
7	chr13:39244482..39246478-chr13:39258303..39260583,2	MCF-7	breast:
8	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

No data

Variant related genes	Relation type
FREM2	TF binding region
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11147726	0.92[AFR][1000 genomes]
rs11147727	0.92[AFR][1000 genomes]
rs11147728	0.92[AFR][1000 genomes]
rs17058420	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17058443	0.99[AFR][1000 genomes]
rs17058452	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs17058513	0.88[AFR][1000 genomes]
rs41418944	0.82[AFR][1000 genomes]
rs56359648	0.83[AMR][1000 genomes]
rs57001791	0.92[AFR][1000 genomes]
rs59255961	0.91[AFR][1000 genomes]
rs59593155	1.00[AMR][1000 genomes]
rs59939899	0.92[AFR][1000 genomes]
rs60698466	0.85[AFR][1000 genomes]
rs6563630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7336865	0.99[AFR][1000 genomes]
rs7982877	1.00[AMR][1000 genomes]
rs7984183	0.85[AFR][1000 genomes]
rs7984232	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs7997838	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7999409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8002488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9671014	0.88[AFR][1000 genomes];1.00[AMR][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	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39255200-39259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:39255200-39260200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:39255800-39260200	Weak transcription	Adipose Nuclei	Adipose
4	chr13:39257800-39260000	Enhancers	Fetal Intestine Large	intestine
5	chr13:39258000-39260400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:39259000-39259800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr13:39259000-39259800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:39259000-39259800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr13:39259000-39260000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:39259000-39260000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:39259000-39260000	Enhancers	Fetal Intestine Small	intestine
12	chr13:39259000-39260200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:39259000-39260200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr13:39259600-39259800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:39259600-39259800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr13:39259600-39259800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr13:39259600-39259800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr13:39259600-39259800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr13:39259600-39259800	Flanking Active TSS	Fetal Kidney	kidney
20	chr13:39259600-39260000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:39259600-39260000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:39259600-39260000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:39259600-39260200	Enhancers	Brain Germinal Matrix	brain
24	chr13:39259600-39260200	Enhancers	HMEC	breast
25	chr13:39259600-39260600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr13:39259600-39260600	Enhancers	Placenta	Placenta
27	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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