Variant report

Variant	rs7322083
Chromosome Location	chr13:92050246-92050247
allele	A/G
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	IRF1	chr13:92050184-92051070	K562	blood:	n/a	chr13:92051029-92051043
2	JUND	chr13:92050197-92051318	K562	blood:	n/a	n/a
3	ZMIZ1	chr13:92050062-92051285	K562	blood:	n/a	n/a
4	ZNF143	chr13:92050178-92050894	K562	blood:	n/a	n/a
5	STAT5A	chr13:92050063-92050814	K562	blood:	n/a	chr13:92050542-92050550 chr13:92050098-92050106
6	ZC3H11A	chr13:92049717-92051180	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:92050067..92050884-chr13:92058646..92059591,2	K562	blood:

Variant related genes	Relation type
GPC5	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1324062	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224851	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7318578	0.85[CHD][hapmap]
rs7328355	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330545	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515923	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9523325	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9523328	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7322083	GPC5	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92049800-92050400	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr13:92049800-92050400	Bivalent Enhancer	Fetal Lung	lung
3	chr13:92049800-92050600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr13:92050000-92050400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr13:92050000-92050400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr13:92050000-92050400	Enhancers	Hela-S3	cervix
7	chr13:92050200-92050400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr13:92050200-92050400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:92050200-92050400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:92050200-92050400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:92050200-92050400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr13:92050200-92050400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr13:92050200-92050400	Enhancers	Brain Substantia Nigra	brain
14	chr13:92050200-92050400	Bivalent Enhancer	Fetal Kidney	kidney
15	chr13:92050200-92050600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr13:92050200-92050600	Enhancers	Colon Smooth Muscle	Colon
17	chr13:92050200-92050600	Flanking Active TSS	GM12878-XiMat	blood
18	chr13:92050200-92050800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
19	chr13:92050200-92051200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:92050200-92052600	Active TSS	Brain Cingulate Gyrus	brain

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