Variant report

Variant	rs11217426
Chromosome Location	chr11:119590878-119590879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:119587850..119589350-chr11:119589562..119592404,2	MCF-7	breast:
2	chr11:119590103..119594091-chr11:119595863..119600251,5	MCF-7	breast:
3	chr11:119554400..119557288-chr11:119589688..119591871,2	MCF-7	breast:
4	chr11:119582343..119585155-chr11:119589653..119593219,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10790339	0.84[EUR][1000 genomes]
rs10892444	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10892445	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10892446	0.80[EUR][1000 genomes]
rs11217429	0.86[EUR][1000 genomes]
rs11217430	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11217437	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11217438	0.80[EUR][1000 genomes]
rs11217440	0.80[EUR][1000 genomes]
rs11217441	0.80[EUR][1000 genomes]
rs11217442	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217448	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11607610	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12361192	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12418662	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12421434	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12421466	0.81[EUR][1000 genomes]
rs12786505	0.89[EUR][1000 genomes]
rs12793075	0.81[CEU][hapmap];0.85[GIH][hapmap];0.80[EUR][1000 genomes]
rs12796806	0.80[EUR][1000 genomes]
rs12800445	0.86[EUR][1000 genomes]
rs1876795	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2136420	0.85[EUR][1000 genomes]
rs2136421	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2368936	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs35248712	0.80[EUR][1000 genomes]
rs4245206	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4489755	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4505073	0.81[CEU][hapmap]
rs4936496	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs4938718	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs4938720	0.80[EUR][1000 genomes]
rs58136657	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6589770	0.89[EUR][1000 genomes]
rs73006720	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952366	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9666263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11217426	DDX6	cis	cerebellum	SCAN
rs11217426	HSPA8	cis	parietal	SCAN
rs11217426	SORL1	cis	cerebellum	SCAN
rs11217426	YARS2	trans	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119572600-119592000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:119573000-119591800	Weak transcription	Left Ventricle	heart
3	chr11:119574000-119597200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:119575200-119591600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:119580800-119597000	Weak transcription	Lung	lung
6	chr11:119581000-119591600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:119581000-119591600	Weak transcription	Colonic Mucosa	Colon
8	chr11:119582200-119593600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:119584600-119591600	Weak transcription	Fetal Heart	heart
10	chr11:119584600-119591800	Weak transcription	Placenta	Placenta
11	chr11:119584800-119592000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:119585200-119591200	Weak transcription	Stomach Mucosa	stomach
13	chr11:119585200-119591800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:119585200-119592000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:119585200-119596600	Weak transcription	Primary B cells from cord blood	blood
16	chr11:119586200-119595200	Genic enhancers	Esophagus	oesophagus
17	chr11:119586400-119597600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:119587800-119592000	Weak transcription	Fetal Intestine Large	intestine
19	chr11:119588400-119591600	Weak transcription	Fetal Kidney	kidney
20	chr11:119588400-119596800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:119588600-119592400	Weak transcription	Gastric	stomach
22	chr11:119588600-119597400	Weak transcription	NH-A	brain
23	chr11:119588800-119591400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:119589000-119591200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:119589000-119592000	Weak transcription	Brain Anterior Caudate	brain
26	chr11:119589000-119594800	Weak transcription	Brain Germinal Matrix	brain
27	chr11:119589200-119591200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:119589200-119591200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:119589200-119591200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:119589200-119591400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:119589200-119591400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:119589200-119591600	Strong transcription	Fetal Intestine Small	intestine
33	chr11:119589200-119591800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:119589200-119594600	Weak transcription	Fetal Brain Male	brain
35	chr11:119589200-119596800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:119589400-119591400	Weak transcription	Spleen	Spleen
37	chr11:119589400-119591600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:119589400-119591600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:119589600-119591200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr11:119589600-119591600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:119589600-119591600	Weak transcription	HepG2	liver
42	chr11:119589600-119595600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:119589600-119597400	Weak transcription	Liver	Liver
44	chr11:119590000-119591000	Genic enhancers	HMEC	breast
45	chr11:119590200-119595000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:119590400-119591000	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:119590400-119591200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr11:119590400-119592200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:119590400-119592200	Strong transcription	Fetal Stomach	stomach
50	chr11:119590400-119592400	Genic enhancers	NHEK	skin

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