Variant report

Variant	rs7936879
Chromosome Location	chr11:47976882-47976883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10838791	0.80[ASN][1000 genomes]
rs10838794	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs11039467	0.85[CEU][hapmap]
rs55724440	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61914662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114011	1.00[ASW][hapmap]
rs7927445	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7936879	ARFGAP2	cis	cerebellum	SCAN
rs7936879	SLC39A13	cis	cerebellum	SCAN
rs7936879	MDK	cis	parietal	SCAN
rs7936879	C1QTNF4	cis	multi-tissue	Pritchard
rs7936879	LOC646813	cis	cerebellum	SCAN
rs7936879	C1QTNF4	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47970800-47989200	Weak transcription	A549	lung
2	chr11:47975200-47977000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr11:47976600-47977400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr11:47976600-47977400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr11:47976600-47977600	Enhancers	GM12878-XiMat	blood
6	chr11:47976800-47977000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr11:47976800-47977000	Enhancers	Spleen	Spleen
8	chr11:47976800-47977200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:47976800-47977200	Enhancers	Hela-S3	cervix
10	chr11:47976800-47977400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr11:47976800-47977400	Enhancers	Primary B cells from cord blood	blood
12	chr11:47976800-47977400	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:47976800-47977400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:47976800-47977400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr11:47976800-47977400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:47976800-47977400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr11:47976800-47977400	Enhancers	Fetal Intestine Large	intestine
18	chr11:47976800-47977400	Enhancers	Fetal Intestine Small	intestine
19	chr11:47976800-47977400	Enhancers	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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