Variant report

Variant	rs10899401
Chromosome Location	chr11:77431334-77431335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77411140..77414004-chr11:77430290..77433184,2	MCF-7	breast:
2	chr11:77427105..77428718-chr11:77429810..77432005,2	K562	blood:
3	chr11:77427105..77430416-chr11:77430505..77433629,3	K562	blood:

Variant related genes	Relation type
ENSG00000048649	Chromatin interaction
ENSG00000254985	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10466710	0.94[CHB][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs10793257	0.94[CHB][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs108843	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899396	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899397	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899414	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237264	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237279	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12294668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12418931	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783547	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1945747	1.00[CHB][hapmap]
rs2508184	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35711367	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs570786	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs581807	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs582866	0.86[ASN][1000 genomes]
rs584732	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585172	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585721	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs591283	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs598933	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600968	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs601551	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs603462	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs608389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs608539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609151	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs611671	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs647235	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649671	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs658398	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679155	0.82[EUR][1000 genomes]
rs679526	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs685474	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs694893	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7925289	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7929313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7936105	0.83[ASN][1000 genomes]
rs9667706	0.82[EUR][1000 genomes];0.86[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	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10899401	ALG8	cis	cerebellum	SCAN
rs10899401	C11orf67	cis	cerebellum	SCAN
rs10899401	AQP11	cis	parietal	SCAN
rs10899401	NDUFC2	cis	cerebellum	SCAN
rs10899401	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs10899401	KCTD14	cis	cerebellum	SCAN
rs10899401	ALG8	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77389800-77435400	Weak transcription	Psoas Muscle	Psoas
2	chr11:77391600-77442000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:77394600-77435600	Weak transcription	Gastric	stomach
4	chr11:77394600-77441800	Weak transcription	Spleen	Spleen
5	chr11:77394600-77445600	Weak transcription	Esophagus	oesophagus
6	chr11:77394600-77458800	Weak transcription	Small Intestine	intestine
7	chr11:77394800-77462600	Weak transcription	Fetal Heart	heart
8	chr11:77402600-77435800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:77403200-77442200	Weak transcription	Brain Anterior Caudate	brain
10	chr11:77404600-77441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:77406400-77434600	Weak transcription	Fetal Brain Female	brain
12	chr11:77407200-77448000	Weak transcription	K562	blood
13	chr11:77408400-77434200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:77409400-77441600	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:77409600-77432600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:77409600-77435200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:77409600-77435400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:77409600-77435600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:77409600-77441800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:77409600-77453400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:77409600-77458800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:77409600-77478200	Weak transcription	Brain Angular Gyrus	brain
23	chr11:77409800-77432200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:77409800-77434200	Weak transcription	NHLF	lung
25	chr11:77409800-77434600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:77409800-77435400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:77409800-77435400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:77409800-77435600	Weak transcription	Colonic Mucosa	Colon
29	chr11:77409800-77441600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:77409800-77441600	Weak transcription	Aorta	Aorta
31	chr11:77409800-77441800	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:77410400-77477600	Weak transcription	Brain Substantia Nigra	brain
33	chr11:77410800-77435200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr11:77411000-77433800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:77412400-77435200	Weak transcription	Brain Germinal Matrix	brain
36	chr11:77412600-77432600	Weak transcription	Adipose Nuclei	Adipose
37	chr11:77412800-77441800	Weak transcription	Fetal Brain Male	brain
38	chr11:77413200-77432400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:77413400-77435400	Weak transcription	HSMMtube	muscle
40	chr11:77415400-77435200	Weak transcription	Left Ventricle	heart
41	chr11:77415800-77432400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:77415800-77435200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:77416200-77431800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr11:77416800-77432000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:77416800-77435200	Weak transcription	Fetal Kidney	kidney
46	chr11:77416800-77435400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:77416800-77435800	Weak transcription	NHDF-Ad	bronchial
48	chr11:77416800-77441600	Weak transcription	HMEC	breast
49	chr11:77416800-77441800	Weak transcription	NHEK	skin
50	chr11:77417000-77432600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links