Variant report

Variant	rs9900324
Chromosome Location	chr17:38821778-38821779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38821206-38822638	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38803836..38805956-chr17:38820835..38822602,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271876	TF binding region
KRT222	TF binding region
ENSG00000264058	TF binding region
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1029792	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1048572	0.85[EUR][1000 genomes]
rs1048573	0.85[EUR][1000 genomes]
rs12943859	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2008469	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014704	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2109223	0.81[EUR][1000 genomes]
rs2159430	0.80[EUR][1000 genomes]
rs2315020	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2429549	0.81[EUR][1000 genomes]
rs3752026	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890093	0.81[EUR][1000 genomes]
rs4890119	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6503547	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6503549	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7209467	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7209735	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7210983	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7219483	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7223332	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7223354	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8068721	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076587	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917593	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917595	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9896791	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9906785	0.85[EUR][1000 genomes]
rs9915135	0.85[EUR][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	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised 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	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9900324	KRT222	cis	Nerve Tibial	GTEx
rs9900324	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs9900324	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs9900324	KRT24	cis	Esophagus Mucosa	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38820600-38821800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr17:38820600-38821800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr17:38820600-38821800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr17:38821000-38821800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr17:38821000-38821800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr17:38821000-38821800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:38821000-38821800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr17:38821000-38821800	Active TSS	Right Atrium	heart
9	chr17:38821400-38821800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr17:38821400-38821800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr17:38821400-38821800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr17:38821600-38821800	Bivalent Enhancer	Brain Anterior Caudate	brain
13	chr17:38821600-38821800	Weak transcription	Fetal Intestine Large	intestine
14	chr17:38821600-38822000	Weak transcription	Pancreas	Pancrea
15	chr17:38821600-38822200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:38821600-38822400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:38821600-38822400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:38821600-38823200	Enhancers	Duodenum Mucosa	Duodenum
19	chr17:38821600-38823200	Enhancers	A549	lung
20	chr17:38821600-38823400	Enhancers	Liver	Liver
21	chr17:38821600-38824200	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links