Variant report

Variant	rs718439
Chromosome Location	chr11:17834207-17834208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17833715..17836483-chr11:17839806..17843021,3	MCF-7	breast:
2	chr11:17791223..17792205-chr11:17834136..17835260,3	MCF-7	breast:
3	chr11:17802032..17804366-chr11:17833882..17835723,2	MCF-7	breast:
4	chr11:17791549..17792453-chr11:17833752..17834540,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1005008	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10160556	0.90[EUR][1000 genomes]
rs10466421	0.81[AMR][1000 genomes]
rs10766440	0.90[EUR][1000 genomes]
rs10832860	0.86[EUR][1000 genomes]
rs11024415	0.90[CHB][hapmap];0.88[AMR][1000 genomes]
rs11821847	0.90[CHB][hapmap]
rs1548528	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079227	0.92[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2107427	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs2158395	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2158396	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2237943	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237946	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237949	0.96[YRI][hapmap]
rs2237950	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2237952	0.91[EUR][1000 genomes]
rs2283249	0.90[CHB][hapmap]
rs2299632	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2299633	0.90[CHB][hapmap]
rs3802969	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4757589	0.88[CEU][hapmap]
rs4757591	0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs4757593	0.80[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6486398	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6486399	0.88[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7106840	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs7109837	0.86[EUR][1000 genomes]
rs7115183	0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap]
rs7124199	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs765989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929668	0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs7932686	1.00[CHB][hapmap]
rs7935967	0.90[CHB][hapmap]

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	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs718439	SOX6	cis	cerebellum	SCAN
rs718439	MSL3	trans	lymphoblastoid	seeQTL
rs718439	RAB31	trans	lymphoblastoid	seeQTL
rs718439	HBD	trans	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17806000-17837800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
3	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
4	chr11:17808800-17834600	Weak transcription	Aorta	Aorta
5	chr11:17815600-17841400	Weak transcription	HepG2	liver
6	chr11:17818600-17843200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:17825400-17843400	Weak transcription	Lung	lung
8	chr11:17831000-17836200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr11:17831200-17834400	Enhancers	Brain Hippocampus Middle	brain
10	chr11:17831200-17837000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr11:17831200-17849400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:17831400-17834400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr11:17831600-17835600	Enhancers	Fetal Muscle Leg	muscle
14	chr11:17831600-17836400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:17831800-17834600	Enhancers	Fetal Muscle Trunk	muscle
16	chr11:17831800-17835600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:17831800-17835600	Enhancers	Left Ventricle	heart
18	chr11:17832000-17834600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:17832000-17834600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:17832000-17834800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr11:17832000-17849600	Weak transcription	Primary T cells from cord blood	blood
22	chr11:17832200-17835000	Enhancers	Brain Angular Gyrus	brain
23	chr11:17832200-17835200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr11:17832200-17835400	Enhancers	Placenta	Placenta
25	chr11:17832200-17835600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr11:17832200-17835800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:17832200-17835800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:17832400-17835000	Enhancers	Brain Cingulate Gyrus	brain
29	chr11:17832400-17835600	Enhancers	Brain Anterior Caudate	brain
30	chr11:17832400-17835600	Enhancers	Fetal Brain Male	brain
31	chr11:17832400-17836400	Enhancers	Rectal Smooth Muscle	rectum
32	chr11:17832400-17838600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:17832600-17834400	Weak transcription	NH-A	brain
34	chr11:17832800-17834600	Weak transcription	Osteobl	bone
35	chr11:17832800-17834800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:17833000-17835200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr11:17833000-17835600	Enhancers	Stomach Smooth Muscle	stomach
38	chr11:17833000-17836600	Enhancers	Psoas Muscle	Psoas
39	chr11:17833000-17843800	Weak transcription	HSMMtube	muscle
40	chr11:17833200-17834400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:17833200-17835600	Enhancers	Fetal Lung	lung
42	chr11:17833200-17838000	Weak transcription	Right Atrium	heart
43	chr11:17833400-17834400	Enhancers	Fetal Intestine Small	intestine
44	chr11:17833400-17834600	Enhancers	Pancreas	Pancrea
45	chr11:17833400-17834600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr11:17833400-17835000	Enhancers	Gastric	stomach
47	chr11:17833400-17835600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr11:17833600-17834600	Weak transcription	HMEC	breast
49	chr11:17833600-17834600	Weak transcription	NHEK	skin
50	chr11:17833600-17834800	Enhancers	Fetal Kidney	kidney

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