Variant report

Variant	rs2231172
Chromosome Location	chr7:100252918-100252919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100237538..100239749-chr7:100251463..100254292,3	K562	blood:
2	chr7:100243068..100245552-chr7:100251796..100254124,2	K562	blood:

Variant related genes	Relation type
ENSG00000106327	Chromatin interaction
ENSG00000077080	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10487157	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs10953299	0.95[EUR][1000 genomes]
rs10953301	0.81[CHB][hapmap]
rs11520986	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs11764045	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs11766643	0.86[AMR][1000 genomes]
rs11767547	0.87[AMR][1000 genomes]
rs11770389	0.86[AMR][1000 genomes]
rs11770534	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772667	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11974395	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs11979818	0.84[ASW][hapmap];0.90[MEX][hapmap]
rs11983334	0.90[MEX][hapmap]
rs11983745	0.87[AMR][1000 genomes]
rs12532878	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs2075671	0.94[MEX][hapmap]
rs2075672	0.86[JPT][hapmap]
rs2075674	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes]
rs2231170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2272572	0.81[CHB][hapmap]
rs41303510	0.86[AMR][1000 genomes]
rs4727459	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs4729597	0.86[JPT][hapmap]
rs4729601	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729602	0.81[CHB][hapmap];0.95[MEX][hapmap]
rs4729606	0.84[ASW][hapmap];0.85[MEX][hapmap]
rs62482242	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6942733	0.84[ASW][hapmap]
rs6952341	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs6958696	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6969584	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs6969697	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs73156234	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73170760	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7385804	0.86[JPT][hapmap]
rs7786877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7812123	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs7812235	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv607934	chr7:100240505-100271521	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2231172	PERQ1	Cis_1M	lymphoblastoid	RTeQTL
rs2231172	POLR2J	cis	parietal	SCAN
rs2231172	SERPINE1	cis	cerebellum	SCAN
rs2231172	DLX5	cis	cerebellum	SCAN
rs2231172	TSC22D4	cis	parietal	SCAN
rs2231172	GIGYF1	cis	lymphoblastoid	seeQTL
rs2231172	MOSPD3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100241000-100253200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:100252400-100253000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
3	chr7:100252600-100253000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr7:100252600-100253000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
5	chr7:100252600-100253400	Enhancers	Fetal Brain Male	brain
6	chr7:100252600-100253400	Enhancers	Gastric	stomach
7	chr7:100252600-100253600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:100252600-100254400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr7:100252800-100253000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
10	chr7:100252800-100253000	Active TSS	Fetal Brain Female	brain
11	chr7:100252800-100253400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:100252800-100253600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
13	chr7:100252800-100253600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:100252800-100254000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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