Variant report

Variant	rs9897309
Chromosome Location	chr17:17623988-17623989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17621090..17625652-chr17:17628958..17633678,4	K562	blood:
2	chr17:17623309..17626768-chr17:17630272..17633678,3	K562	blood:
3	chr17:17622624..17624957-chr17:17740328..17743276,2	K562	blood:
4	chr17:17591306..17603641-chr17:17622226..17637880,43	MCF-7	breast:
5	chr17:17612154..17614264-chr17:17622183..17624115,2	K562	blood:
6	chr17:17623385..17625295-chr17:17685917..17688281,2	MCF-7	breast:
7	chr17:17582718..17591238-chr17:17621630..17636217,47	MCF-7	breast:
8	chr17:17622227..17624857-chr17:17737770..17740732,3	MCF-7	breast:
9	chr17:17618965..17621163-chr17:17622040..17625612,4	K562	blood:
10	chr17:17616640..17621163-chr17:17622040..17627772,6	K562	blood:
11	chr17:17623498..17628448-chr17:17639518..17645523,5	MCF-7	breast:
12	chr17:17623843..17637985-chr17:17653006..17664308,33	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12940014	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2001884	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2350632	0.85[EUR][1000 genomes]
rs2350633	0.83[EUR][1000 genomes]
rs4496218	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4925092	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4925093	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4925094	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4925096	0.82[EUR][1000 genomes]
rs4925102	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925104	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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];0.95[ASN][1000 genomes]
rs6502613	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs6502615	0.89[CEU][hapmap];0.90[CHD][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs7208561	0.85[CEU][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap]
rs7214245	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7224617	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7224619	0.86[EUR][1000 genomes]
rs7224739	0.85[CEU][hapmap];0.90[CHD][hapmap]
rs7225934	0.86[EUR][1000 genomes]
rs8065154	0.89[CEU][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes]
rs8075153	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs897457	0.87[EUR][1000 genomes]
rs9897044	0.80[EUR][1000 genomes]
rs9897596	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9904468	0.88[EUR][1000 genomes]
rs9906532	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9910411	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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
24	nsv9501	chr17:17623197-17628790	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9897309	TOM1L2	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17613600-17624400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:17616000-17624800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:17616000-17625000	Weak transcription	Brain Germinal Matrix	brain
4	chr17:17616200-17625200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:17616200-17642000	Weak transcription	K562	blood
6	chr17:17617600-17625800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:17617800-17625200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:17618200-17624800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:17618200-17625400	Weak transcription	Brain Substantia Nigra	brain
10	chr17:17618200-17626600	Weak transcription	HSMM	muscle
11	chr17:17618400-17624600	Strong transcription	Fetal Stomach	stomach
12	chr17:17618400-17624800	Weak transcription	Osteobl	bone
13	chr17:17618400-17626800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr17:17618600-17624800	Weak transcription	Fetal Brain Female	brain
15	chr17:17618800-17624800	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:17618800-17625400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr17:17618800-17626000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:17620000-17624800	Weak transcription	Fetal Brain Male	brain
19	chr17:17620200-17625200	Weak transcription	Brain Anterior Caudate	brain
20	chr17:17620400-17625200	Weak transcription	Ovary	ovary
21	chr17:17620400-17625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:17620600-17624800	Weak transcription	Fetal Intestine Large	intestine
23	chr17:17620800-17625000	Enhancers	HepG2	liver
24	chr17:17620800-17626200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr17:17621000-17624800	Strong transcription	Fetal Intestine Small	intestine
26	chr17:17621000-17625400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr17:17621200-17624800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:17621200-17625000	Weak transcription	NHLF	lung
29	chr17:17621200-17626000	Weak transcription	Liver	Liver
30	chr17:17621400-17625600	Enhancers	Right Ventricle	heart
31	chr17:17621600-17624800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:17621600-17625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:17621600-17625200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:17621600-17625200	Weak transcription	Primary T cells from cord blood	blood
35	chr17:17621600-17625800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:17621800-17624000	Enhancers	Pancreas	Pancrea
37	chr17:17621800-17624400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr17:17621800-17624800	Enhancers	Left Ventricle	heart
39	chr17:17621800-17625000	Weak transcription	Fetal Lung	lung
40	chr17:17621800-17625600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:17622000-17624600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:17622000-17625000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:17622000-17625200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:17622000-17626000	Enhancers	Esophagus	oesophagus
45	chr17:17622400-17625800	Weak transcription	GM12878-XiMat	blood
46	chr17:17622400-17625800	Enhancers	HMEC	breast
47	chr17:17622600-17624800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:17622600-17625400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:17622600-17626000	Enhancers	Gastric	stomach
50	chr17:17623000-17624600	Enhancers	Fetal Heart	heart

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