Variant report

Variant	rs1044269
Chromosome Location	chr11:47487740-47487741
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	chr11:47486877..47488981-chr11:47490201..47491950,2	K562	blood:
2	chr11:47486712..47489555-chr11:47586746..47588709,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110536	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10742806	0.94[JPT][hapmap]
rs10742816	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs10769255	0.90[CEU][hapmap]
rs10769267	0.80[ASN][1000 genomes]
rs11039278	0.85[AMR][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11820650	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11821273	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11821860	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11821917	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11822402	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11823490	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11824864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11824971	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11824990	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11827106	0.82[ASN][1000 genomes]
rs11828339	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12419342	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1474056	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs17198158	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17790804	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2138767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2242511	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3729802	0.82[CEU][hapmap]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3740685	0.81[ASN][1000 genomes]
rs3781628	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3824867	0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3847503	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147730	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4282946	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4384349	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4752783	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4752786	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4752829	0.88[JPT][hapmap]
rs4752836	0.81[ASN][1000 genomes]
rs4752837	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4752839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752843	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752992	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56756748	0.80[ASN][1000 genomes]
rs59631865	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60380053	0.80[ASN][1000 genomes]
rs60882887	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60929305	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61000762	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104366	0.80[ASN][1000 genomes]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7105907	0.94[JPT][hapmap]
rs7106142	0.81[ASN][1000 genomes]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7115371	0.80[ASN][1000 genomes]
rs7117277	0.80[ASN][1000 genomes]
rs7119556	0.80[ASN][1000 genomes]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7130693	0.80[ASN][1000 genomes]
rs753812	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7931089	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7948705	0.94[JPT][hapmap]
rs9666924	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9734013	0.80[ASN][1000 genomes]
rs9919526	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1044269	SLC35C1	cis	cerebellum	SCAN
rs1044269	LOC441601	cis	cerebellum	SCAN
rs1044269	ATG13	cis	parietal	SCAN
rs1044269	TTC17	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47457400-47488400	Weak transcription	Gastric	stomach
3	chr11:47471200-47488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:47471400-47489200	Weak transcription	HepG2	liver
5	chr11:47476200-47488200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:47476600-47488400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:47476600-47488600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:47478200-47488400	Weak transcription	Esophagus	oesophagus
9	chr11:47479400-47488200	Weak transcription	Colonic Mucosa	Colon
10	chr11:47479400-47491200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr11:47479600-47489800	Weak transcription	Fetal Kidney	kidney
12	chr11:47479600-47491400	Weak transcription	Aorta	Aorta
13	chr11:47479800-47489000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:47479800-47494400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:47480000-47487800	Strong transcription	Fetal Stomach	stomach
16	chr11:47480000-47510000	Strong transcription	Thymus	Thymus
17	chr11:47480200-47488800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:47480600-47489000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:47480600-47508400	Strong transcription	Fetal Intestine Small	intestine
20	chr11:47480800-47511000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:47480800-47511400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:47481000-47498400	Strong transcription	NHEK	skin
23	chr11:47481400-47488200	Weak transcription	Pancreas	Pancrea
24	chr11:47482200-47488800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:47482200-47489000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr11:47482400-47488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:47482600-47488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:47482600-47488600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:47482800-47488200	Weak transcription	Fetal Heart	heart
30	chr11:47483400-47487800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:47483400-47508800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:47483600-47511400	Strong transcription	Dnd41	blood
33	chr11:47483800-47488000	Weak transcription	Fetal Brain Male	brain
34	chr11:47484000-47488400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:47484200-47489000	Weak transcription	Psoas Muscle	Psoas
36	chr11:47484800-47488400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:47484800-47490800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:47484800-47504800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:47484800-47510600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr11:47484800-47511000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:47485000-47488200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr11:47485000-47488400	Strong transcription	Hela-S3	cervix
43	chr11:47485000-47488600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:47485200-47488600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:47485200-47488800	Strong transcription	Fetal Thymus	thymus
46	chr11:47485200-47511400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:47485400-47488800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:47485400-47504800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr11:47485400-47511400	Strong transcription	Primary B cells from cord blood	blood
50	chr11:47485600-47487800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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