Variant report

Variant	rs11689234
Chromosome Location	chr2:73931716-73931717
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	SPI1	chr2:73931477-73931763	K562	blood:	n/a	chr2:73931672-73931685
2	SPI1	chr2:73931672-73931913	HL-60	blood:	n/a	chr2:73931672-73931685

No.	Distal block	Cell Line	Cell type
1	chr2:73868945..73872912-chr2:73927731..73932752,4	MCF-7	breast:
2	chr2:73931503..73934295-chr2:73936024..73937687,2	MCF-7	breast:
3	chr2:73920861..73923082-chr2:73929614..73932212,2	K562	blood:

Variant related genes	Relation type
ENSG00000204872	TF binding region
ENSG00000144035	Chromatin interaction
ENSG00000163016	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11126411	0.93[CHB][hapmap]
rs11126414	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs11674212	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12233112	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12478871	0.92[CHB][hapmap]
rs12991161	0.88[CHB][hapmap]
rs12998980	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs13027816	0.88[CHB][hapmap]
rs17009372	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2001436	0.89[CHB][hapmap]
rs2001490	0.89[CHB][hapmap]
rs2280506	0.88[CHB][hapmap]
rs2280507	0.93[CHB][hapmap]
rs2421586	0.88[CHB][hapmap]
rs2421587	0.88[CHB][hapmap]
rs2567601	0.80[CEU][hapmap]
rs2947845	0.88[CHB][hapmap]
rs4627598	0.88[CHB][hapmap]
rs4852311	0.93[CHB][hapmap]
rs4852951	0.88[CHB][hapmap]
rs4852954	0.88[CHB][hapmap]
rs4852974	0.82[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs6744273	0.88[CHB][hapmap]
rs7570683	0.88[CHB][hapmap]
rs7579068	0.88[CHB][hapmap]
rs7607989	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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 target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription 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 target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv874277	chr2:73870010-73931971	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874278	chr2:73870010-73931971	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3426494	chr2:73876125-73939153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3460808	chr2:73877074-73940302	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3460809	chr2:73877074-73940302	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv2753082	chr2:73891045-73955545	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv979022	chr2:73897805-73932073	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv34157	chr2:73901718-73949151	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 target site	33 gene(s)	inside rSNPs	diseases
16	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv1003153	chr2:73927235-73975416	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11689234	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11689234	ALMS1	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73900600-73954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells	blood
3	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:73927200-73932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:73928400-73936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:73929200-73936400	Enhancers	Fetal Intestine Large	intestine
8	chr2:73929800-73931800	Weak transcription	K562	blood
9	chr2:73929800-73934200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:73929800-73934400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73929800-73934600	Weak transcription	Colonic Mucosa	Colon
12	chr2:73930400-73932200	Enhancers	Ovary	ovary
13	chr2:73930600-73932800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr2:73930800-73932000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr2:73931000-73932000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:73931000-73933800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:73931200-73932200	Weak transcription	Lung	lung
18	chr2:73931400-73932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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