Variant report

Variant	rs7213879
Chromosome Location	chr17:17621571-17621572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17621090..17625652-chr17:17628958..17633678,4	K562	blood:
2	chr17:17619763..17622601-chr17:17723759..17726284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12938840	0.86[ASN][1000 genomes]
rs12938914	0.85[ASN][1000 genomes]
rs2001421	0.84[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs2350962	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2882552	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4074643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244601	0.87[JPT][hapmap]
rs4636969	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4924813	0.86[JPT][hapmap]
rs4925103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4995264	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs720856	0.81[JPT][hapmap]
rs7209595	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8071107	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[YRI][hapmap]
rs9900148	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9905702	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9907986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS 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	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	80 gene(s)	inside rSNPs	diseases
11	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
12	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
18	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
19	nsv907756	chr17:17619859-17747289	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
20	nsv522668	chr17:17619859-17752809	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
21	nsv907757	chr17:17619859-17752809	Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
22	nsv907758	chr17:17619859-17782404	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
23	nsv907759	chr17:17619859-17802478	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7213879	LLGL1	cis	parietal	SCAN
rs7213879	TOM1L2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17613400-17621600	Weak transcription	Thymus	Thymus
2	chr17:17613600-17624400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:17616000-17624800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:17616000-17625000	Weak transcription	Brain Germinal Matrix	brain
5	chr17:17616200-17625200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr17:17616200-17642000	Weak transcription	K562	blood
7	chr17:17617000-17622000	Enhancers	Fetal Thymus	thymus
8	chr17:17617600-17623400	Weak transcription	Colonic Mucosa	Colon
9	chr17:17617600-17625800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr17:17617800-17625200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:17618000-17621800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:17618000-17622400	Weak transcription	HMEC	breast
13	chr17:17618000-17623200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr17:17618000-17623400	Weak transcription	Hela-S3	cervix
15	chr17:17618200-17621600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr17:17618200-17622400	Weak transcription	NHEK	skin
17	chr17:17618200-17622600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:17618200-17624800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:17618200-17625400	Weak transcription	Brain Substantia Nigra	brain
20	chr17:17618200-17626600	Weak transcription	HSMM	muscle
21	chr17:17618400-17623600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:17618400-17624600	Strong transcription	Fetal Stomach	stomach
23	chr17:17618400-17624800	Weak transcription	Osteobl	bone
24	chr17:17618400-17626800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:17618600-17622400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:17618600-17623200	Weak transcription	Right Atrium	heart
27	chr17:17618600-17623400	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:17618600-17623600	Weak transcription	Adipose Nuclei	Adipose
29	chr17:17618600-17623800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:17618600-17624800	Weak transcription	Fetal Brain Female	brain
31	chr17:17618800-17623200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:17618800-17624800	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:17618800-17625400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr17:17618800-17626000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:17619200-17623200	Weak transcription	Lung	lung
36	chr17:17619400-17623400	Weak transcription	Stomach Mucosa	stomach
37	chr17:17619600-17621600	Enhancers	Primary T cells from cord blood	blood
38	chr17:17619600-17621800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr17:17619800-17621600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:17619800-17621800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:17619800-17621800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:17619800-17623200	Weak transcription	Brain Angular Gyrus	brain
43	chr17:17620000-17624800	Weak transcription	Fetal Brain Male	brain
44	chr17:17620200-17621800	Weak transcription	Gastric	stomach
45	chr17:17620200-17622000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:17620200-17622000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:17620200-17623000	Weak transcription	Fetal Heart	heart
48	chr17:17620200-17625200	Weak transcription	Brain Anterior Caudate	brain
49	chr17:17620400-17621800	Weak transcription	Left Ventricle	heart
50	chr17:17620400-17622400	Enhancers	GM12878-XiMat	blood

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