Variant report

Variant	rs10169164
Chromosome Location	chr2:47478791-47478792
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47477055..47479211-chr2:47498989..47500882,2	MCF-7	breast:
2	chr2:47426189..47428111-chr2:47478013..47479523,2	MCF-7	breast:
3	chr2:47471172..47473317-chr2:47476209..47479649,3	MCF-7	breast:
4	chr2:47401347..47405305-chr2:47474858..47480763,8	MCF-7	breast:
5	chr2:47418320..47420689-chr2:47477088..47480602,4	MCF-7	breast:
6	chr2:47400916..47405681-chr2:47469986..47480951,19	K562	blood:
7	chr2:47478076..47480290-chr2:47491113..47492985,2	K562	blood:
8	chr2:47441944..47444316-chr2:47476312..47479303,2	MCF-7	breast:
9	chr2:47478646..47481044-chr2:47483765..47486319,2	MCF-7	breast:
10	chr2:47476493..47480049-chr2:47496667..47500826,6	MCF-7	breast:
11	chr2:47400516..47406880-chr2:47471949..47486822,24	K562	blood:
12	chr2:47450507..47453723-chr2:47476153..47479003,3	MCF-7	breast:
13	chr2:47409469..47411339-chr2:47477135..47479722,2	MCF-7	breast:
14	chr2:47477685..47479668-chr2:47480909..47483654,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1995109	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1995110	0.90[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952879	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4953482	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4953483	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4953484	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4953485	0.91[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7560679	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598661	0.88[CEU][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs904160	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10169164	LOC100129726	cis	parietal	SCAN
rs10169164	STON1-GTF2A1L	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47475800-47478800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:47476000-47479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47476600-47483800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:47476800-47483600	Weak transcription	A549	lung
5	chr2:47477000-47483400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:47477000-47483400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:47477000-47491400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:47477200-47491200	Weak transcription	Brain Anterior Caudate	brain
9	chr2:47477400-47479600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:47477600-47478800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:47477600-47478800	Enhancers	K562	blood
12	chr2:47477800-47480000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:47478000-47483600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:47478200-47478800	Enhancers	Hela-S3	cervix
15	chr2:47478200-47479400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:47478200-47483600	Weak transcription	NH-A	brain
17	chr2:47478400-47478800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:47478600-47483800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links