Variant report

Variant	rs500531
Chromosome Location	chr11:64487019-64487020
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64485321..64487763-chr11:64492091..64495003,2	K562	blood:
2	chr11:64485640..64487151-chr11:64515776..64517984,2	MCF-7	breast:
3	chr11:64485672..64488139-chr11:64489786..64491520,2	MCF-7	breast:
4	chr11:64479124..64481401-chr11:64485906..64488788,2	K562	blood:
5	chr11:64485500..64487701-chr11:64488311..64491830,5	K562	blood:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000068976	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10792443	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10897518	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11231825	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11231845	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11606370	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11607663	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2277311	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2360872	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2360873	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2666559	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2666563	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35195142	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3825016	0.89[CEU][hapmap]
rs3825018	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs475642	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs477138	0.84[JPT][hapmap]
rs492175	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4930556	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs495130	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504915	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs505802	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs506338	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs518053	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519090	0.90[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524023	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs526338	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs528211	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs538737	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs544838	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs555456	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7102344	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7932437	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs80841	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs893006	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs9734313	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
6	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
17	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
19	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs500531	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs500531	NRXN2	cis	lung	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64480400-64489800	Enhancers	Fetal Brain Male	brain
2	chr11:64482600-64489000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:64485000-64487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:64485600-64489000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:64485800-64487400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:64485800-64488200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:64486000-64488400	Weak transcription	Spleen	Spleen
8	chr11:64486400-64487200	Weak transcription	Fetal Brain Female	brain
9	chr11:64486400-64488600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:64487000-64487200	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr11:64487000-64490600	Weak transcription	K562	blood

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