Variant report

Variant	rs601887
Chromosome Location	chr11:65590713-65590714
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	chr11:65478815..65481669-chr11:65588844..65590802,2	K562	blood:
2	chr11:65588417..65591084-chr11:65617236..65619160,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CFL1-2	chr11:65590493-65591574	NONHSAT022222

Variant related genes	Relation type
ENSG00000172977	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10791825	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791826	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10791828	0.82[JPT][hapmap]
rs10896049	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896055	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151515	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1204771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1204772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420336	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13817	0.88[GIH][hapmap]
rs1939212	0.85[GIH][hapmap]
rs4930162	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930322	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930325	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558114	0.88[GIH][hapmap]
rs56169730	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836187	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60678003	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895685	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630303	0.88[GIH][hapmap]
rs635375	0.88[GIH][hapmap]
rs646675	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	0.88[GIH][hapmap]
rs652021	0.88[GIH][hapmap]
rs656040	0.88[GIH][hapmap]
rs6591191	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659857	0.88[GIH][hapmap]
rs665306	0.88[GIH][hapmap]
rs668356	0.88[GIH][hapmap]
rs7112754	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114014	0.84[GIH][hapmap]
rs7114237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924752	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs601887	GPHA2	cis	parietal	SCAN
rs601887	MACROD1	cis	parietal	SCAN
rs601887	ANKRD13D	cis	parietal	SCAN
rs601887	NEAT1	cis	lymphoblastoid	seeQTL
rs601887	CARNS1	cis	cerebellum	SCAN
rs601887	SNORD27	cis	cerebellum	SCAN
rs601887	EHD1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65585800-65600200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:65585800-65600600	Weak transcription	Small Intestine	intestine
3	chr11:65586000-65591200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:65586200-65594400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:65588400-65591400	Enhancers	Colonic Mucosa	Colon
6	chr11:65589000-65590800	Weak transcription	Gastric	stomach
7	chr11:65589000-65594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:65589000-65594600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:65589200-65590800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:65590000-65590800	Flanking Active TSS	Fetal Intestine Small	intestine
11	chr11:65590200-65591000	Bivalent Enhancer	HepG2	liver
12	chr11:65590200-65591400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr11:65590200-65591400	Enhancers	Stomach Mucosa	stomach
14	chr11:65590400-65591600	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr11:65590400-65591600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr11:65590600-65590800	Enhancers	Liver	Liver
17	chr11:65590600-65590800	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr11:65590600-65591400	Enhancers	Pancreas	Pancrea

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