Variant report

Variant	rs4489755
Chromosome Location	chr11:119605480-119605481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:119600071..119603672-chr11:119605358..119609568,4	MCF-7	breast:
2	chr11:119586554..119590249-chr11:119604143..119607234,3	K562	blood:
3	chr11:119599940..119602278-chr11:119603563..119606152,2	K562	blood:
4	chr11:119598556..119602502-chr11:119605282..119610930,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2523D13.1.1-1	chr11:119602991-119609426	FPKM1_group_5475_transcript_3

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction
ENSG00000254854	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10790339	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10892444	0.88[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10892445	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892446	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11217426	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11217429	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11217430	0.92[EUR][1000 genomes]
rs11217434	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11217437	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11217438	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11217440	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11217441	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11217442	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11217448	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11607610	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12361192	0.90[EUR][1000 genomes]
rs12418662	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12421434	0.85[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12421466	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12786505	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12793075	0.85[CEU][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12796806	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12797914	0.85[EUR][1000 genomes]
rs12800445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1876795	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2136420	0.84[EUR][1000 genomes]
rs2136421	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2368936	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35248712	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4245206	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4505073	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4936496	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4938718	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4938719	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4938720	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58136657	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6589770	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73006720	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7952366	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9666263	0.96[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1037739	chr11:119592989-119630641	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4489755	HSPA8	cis	parietal	SCAN
rs4489755	SORL1	cis	cerebellum	SCAN
rs4489755	DDX6	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119600800-119605800	Weak transcription	Brain Germinal Matrix	brain
2	chr11:119601200-119612000	Weak transcription	Esophagus	oesophagus
3	chr11:119601200-119612200	Weak transcription	Right Atrium	heart
4	chr11:119601400-119610200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:119601400-119612200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:119601400-119612200	Weak transcription	HMEC	breast
7	chr11:119601600-119610600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:119601600-119612000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:119601600-119612000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:119601600-119612200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:119601800-119612000	Weak transcription	Spleen	Spleen
12	chr11:119601800-119612200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:119601800-119612200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:119603400-119610000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:119605200-119606000	Enhancers	Fetal Intestine Large	intestine
16	chr11:119605200-119606200	Enhancers	Duodenum Mucosa	Duodenum
17	chr11:119605200-119606200	Enhancers	Pancreas	Pancrea
18	chr11:119605400-119605800	Enhancers	HUVEC	blood vessel
19	chr11:119605400-119606200	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr11:119605400-119606200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr11:119605400-119612200	Enhancers	Fetal Intestine Small	intestine

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