Variant report

Variant	rs1467051
Chromosome Location	chr11:119568301-119568302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:119568263..119570489-chr11:119571275..119572812,2	K562	blood:
2	chr11:119551416..119553458-chr11:119566192..119569088,2	MCF-7	breast:
3	chr11:119553834..119555975-chr11:119568134..119570409,2	MCF-7	breast:
4	chr11:119567595..119569306-chr11:119571218..119572844,2	MCF-7	breast:
5	chr11:119568098..119571267-chr11:119595317..119602165,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254854	Chromatin interaction
ENSG00000110400	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10790331	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10790332	0.88[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10790335	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10892433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1110166	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11217414	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11217415	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11825206	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1533051	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2006949	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2015078	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2292293	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3902806	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3935405	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935406	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4623916	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936492	0.92[CEU][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4936493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4936494	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4936495	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4938708	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4938709	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4938710	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4938711	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6589769	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7110874	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7111290	0.92[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs7122134	0.88[CEU][hapmap]
rs7124934	0.81[EUR][1000 genomes]
rs715849	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7924573	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7932832	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7933848	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7945395	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7945424	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950059	1.00[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs885429	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs885430	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906830	0.88[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv984471	chr11:119505802-119568473	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv468880	chr11:119564496-119588062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv556471	chr11:119564496-119588062	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1467051	C1QTNF5	cis	parietal	SCAN
rs1467051	RPS25	cis	parietal	SCAN
rs1467051	UPK2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119555800-119568800	Weak transcription	Left Ventricle	heart
2	chr11:119556000-119568600	Weak transcription	Right Atrium	heart
3	chr11:119556000-119571600	Weak transcription	NHLF	lung
4	chr11:119559800-119570200	Enhancers	Fetal Thymus	thymus
5	chr11:119560400-119569600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:119561000-119580600	Weak transcription	Fetal Kidney	kidney
7	chr11:119561400-119568800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr11:119561800-119568400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr11:119561800-119568800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr11:119561800-119577600	Enhancers	Brain Hippocampus Middle	brain
11	chr11:119562000-119568600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr11:119562000-119578400	Enhancers	Duodenum Mucosa	Duodenum
13	chr11:119562400-119571000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:119562400-119571000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr11:119563000-119568600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:119563200-119578400	Genic enhancers	Fetal Intestine Small	intestine
17	chr11:119563400-119568400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr11:119563600-119574000	Enhancers	Placenta	Placenta
19	chr11:119564200-119578400	Enhancers	Fetal Intestine Large	intestine
20	chr11:119564800-119571800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr11:119565000-119568400	Weak transcription	Lung	lung
22	chr11:119565000-119569400	Weak transcription	Fetal Brain Female	brain
23	chr11:119565200-119582600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:119565400-119569400	Weak transcription	Brain Germinal Matrix	brain
25	chr11:119565400-119571400	Weak transcription	NH-A	brain
26	chr11:119565400-119571600	Weak transcription	Primary B cells from cord blood	blood
27	chr11:119565800-119568600	Weak transcription	Gastric	stomach
28	chr11:119565800-119569600	Weak transcription	Brain Anterior Caudate	brain
29	chr11:119565800-119569800	Weak transcription	Pancreas	Pancrea
30	chr11:119565800-119572400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:119566200-119568400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr11:119566200-119568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:119566400-119568600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:119566400-119569400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:119566400-119569600	Weak transcription	Brain Angular Gyrus	brain
36	chr11:119566400-119569800	Weak transcription	Liver	Liver
37	chr11:119566600-119569000	Weak transcription	Brain Substantia Nigra	brain
38	chr11:119567000-119568600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr11:119567000-119572400	Enhancers	Stomach Mucosa	stomach
40	chr11:119567200-119568600	Enhancers	H9 Cell Line	embryonic stem cell
41	chr11:119567200-119568800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr11:119567200-119569000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:119567200-119569400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:119567200-119571800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr11:119567200-119573200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr11:119567200-119573600	Enhancers	Small Intestine	intestine
47	chr11:119567400-119568400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:119567400-119568600	Weak transcription	Esophagus	oesophagus
49	chr11:119567400-119569800	Weak transcription	Spleen	Spleen
50	chr11:119567400-119573400	Enhancers	Sigmoid Colon	Sigmoid Colon

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