Variant report

Variant	rs603462
Chromosome Location	chr11:77577864-77577865
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77575598..77577127-chr11:77577485..77580185,2	K562	blood:
2	chr11:77574596..77578176-chr11:77582421..77584641,3	K562	blood:
3	chr11:77576100..77579696-chr11:77579769..77582425,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THRSP-6	chr11:77576824-77578177	NONHSAT023237

Variant related genes	Relation type
ENSG00000254459	Chromatin interaction
ENSG00000255449	Chromatin interaction
ENSG00000241782	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs108843	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899396	0.85[ASN][1000 genomes]
rs10899397	0.85[ASN][1000 genomes]
rs10899401	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]
rs10899414	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237264	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237279	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12294668	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12418931	0.85[ASN][1000 genomes]
rs1783547	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508184	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35711367	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945228	0.86[GIH][hapmap];0.90[MEX][hapmap]
rs570786	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs581807	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582866	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584732	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585172	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585721	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591283	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598933	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600968	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601551	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609151	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647235	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649671	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658398	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675925	0.84[AFR][1000 genomes]
rs679155	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs679526	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685474	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694893	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925289	0.85[ASN][1000 genomes]
rs7929313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7936105	0.93[ASN][1000 genomes]
rs9667706	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs603462	THRSP	cis	cerebellum	SCAN
rs603462	AQP11	cis	parietal	SCAN
rs603462	NDUFC2	cis	cerebellum	SCAN
rs603462	ALG8	cis	parietal	SCAN
rs603462	KCTD14	cis	cerebellum	SCAN
rs603462	ALG8	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77566000-77592600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:77566200-77579800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:77566200-77580000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:77566200-77580400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:77566200-77580600	Weak transcription	HSMM	muscle
7	chr11:77566200-77582000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:77566200-77582600	Weak transcription	Colonic Mucosa	Colon
9	chr11:77566200-77583200	Weak transcription	Pancreas	Pancrea
10	chr11:77566200-77589000	Weak transcription	NHLF	lung
11	chr11:77566200-77589600	Weak transcription	Esophagus	oesophagus
12	chr11:77566200-77594600	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:77566400-77582000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr11:77566400-77582800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:77566400-77583000	Weak transcription	Spleen	Spleen
16	chr11:77566600-77580200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:77566800-77580200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:77566800-77587800	Weak transcription	A549	lung
19	chr11:77567000-77580600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:77567000-77581800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:77567000-77582600	Weak transcription	HUVEC	blood vessel
22	chr11:77567000-77586600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:77567400-77582600	Weak transcription	Placenta	Placenta
24	chr11:77567600-77582600	Weak transcription	Primary T cells from cord blood	blood
25	chr11:77567600-77589600	Weak transcription	HepG2	liver
26	chr11:77567800-77579600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:77567800-77580600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:77567800-77582400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:77567800-77582600	Weak transcription	Primary B cells from cord blood	blood
30	chr11:77567800-77582800	Weak transcription	Brain Substantia Nigra	brain
31	chr11:77567800-77582800	Weak transcription	Fetal Brain Female	brain
32	chr11:77567800-77589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:77567800-77594800	Weak transcription	Brain Angular Gyrus	brain
34	chr11:77568000-77579800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr11:77568000-77579800	Weak transcription	Thymus	Thymus
36	chr11:77568000-77580400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:77568000-77580400	Weak transcription	Aorta	Aorta
38	chr11:77568000-77580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:77568000-77580600	Weak transcription	GM12878-XiMat	blood
40	chr11:77568000-77580800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:77568000-77582400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:77568000-77582800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:77568000-77583000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:77568000-77586800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:77568000-77587000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:77568200-77579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:77568200-77579800	Weak transcription	Fetal Thymus	thymus
48	chr11:77568200-77580000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:77568200-77582600	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:77568200-77583000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links