Variant report

Variant	rs17053844
Chromosome Location	chr13:53625421-53625422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12864008	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12865218	0.89[ASN][1000 genomes]
rs12866736	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12868253	0.93[ASN][1000 genomes]
rs12876387	0.90[ASN][1000 genomes]
rs12877178	0.89[ASN][1000 genomes]
rs17053814	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17053823	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17053849	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053872	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891947	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275840	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2799344	0.83[ASN][1000 genomes]
rs2799345	0.88[ASN][1000 genomes]
rs34110102	0.99[ASN][1000 genomes]
rs34162017	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34163916	0.83[ASN][1000 genomes]
rs34211399	0.89[ASN][1000 genomes]
rs34298498	0.93[ASN][1000 genomes]
rs34330988	0.92[ASN][1000 genomes]
rs34374288	0.99[ASN][1000 genomes]
rs34642277	0.88[ASN][1000 genomes]
rs34708622	0.85[ASN][1000 genomes]
rs35003538	0.83[ASN][1000 genomes]
rs35007240	0.83[ASN][1000 genomes]
rs35121580	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35137422	0.90[ASN][1000 genomes]
rs35226075	0.92[ASN][1000 genomes]
rs35397855	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35472513	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35559066	0.87[ASN][1000 genomes]
rs35575822	0.89[ASN][1000 genomes]
rs35625606	0.90[ASN][1000 genomes]
rs35666947	0.92[ASN][1000 genomes]
rs35727089	0.92[ASN][1000 genomes]
rs35756659	0.92[ASN][1000 genomes]
rs35765587	0.88[ASN][1000 genomes]
rs36081995	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs57454139	0.83[ASN][1000 genomes]
rs59345770	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs59513810	0.92[ASN][1000 genomes]
rs61950074	0.82[ASN][1000 genomes]
rs61950491	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61950492	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61950504	0.88[ASN][1000 genomes]
rs61950522	0.83[ASN][1000 genomes]
rs74086489	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv832613	chr13:53524319-53687188	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53609000-53626400	Weak transcription	Small Intestine	intestine
2	chr13:53610800-53628800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:53619200-53626600	Weak transcription	Gastric	stomach
4	chr13:53619400-53633000	Weak transcription	Pancreas	Pancrea
5	chr13:53619600-53626400	Weak transcription	Stomach Mucosa	stomach
6	chr13:53620200-53626600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:53621400-53626600	Weak transcription	Fetal Stomach	stomach
8	chr13:53621600-53626400	Weak transcription	Fetal Muscle Leg	muscle
9	chr13:53624600-53625800	Weak transcription	Fetal Kidney	kidney
10	chr13:53624600-53626400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:53625000-53626200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:53625000-53638800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr13:53625200-53626400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:53625400-53626400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links