Variant report

Variant	rs4496218
Chromosome Location	chr17:17587521-17587522
allele	G/T
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17586455..17590031-chr17:17707371..17710346,3	MCF-7	breast:
2	chr17:17581707..17587972-chr17:17684185..17691006,14	MCF-7	breast:
3	chr17:17582541..17589441-chr17:17738170..17742091,10	K562	blood:
4	chr17:17584674..17588119-chr17:17738170..17742427,6	K562	blood:
5	chr17:17583171..17587600-chr17:17683205..17687633,5	MCF-7	breast:
6	chr17:17580850..17587926-chr17:17737733..17744809,17	MCF-7	breast:
7	chr17:17584818..17588540-chr17:17752581..17756325,4	K562	blood:
8	chr17:17321553..17324468-chr17:17587073..17589435,2	MCF-7	breast:
9	chr17:17585146..17587854-chr17:17712160..17713787,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED9-4	chr17:17586860-17588364	NONHSAT146100

No data

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000175662	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12940014	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2001884	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2350632	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2350633	0.91[EUR][1000 genomes]
rs4925092	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4925093	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4925094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925096	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4925102	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4925104	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4925105	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6502613	0.92[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs6502615	0.89[CEU][hapmap]
rs7208561	0.85[CEU][hapmap]
rs7214245	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7224617	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7224619	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7224739	0.85[CEU][hapmap]
rs7225934	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065154	0.89[CEU][hapmap]
rs8075153	0.89[CEU][hapmap]
rs897457	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9897044	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9897309	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs9897596	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9904468	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9906532	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv543239	chr17:17580295-17599851	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv907755	chr17:17581184-17610587	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4496218	TOM1L2	cis	parietal	SCAN
rs4496218	FAM106A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17586400-17588800	Enhancers	Fetal Brain Male	brain
2	chr17:17586600-17590800	Enhancers	Stomach Mucosa	stomach
3	chr17:17586800-17587600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:17586800-17587600	Enhancers	Brain Substantia Nigra	brain
5	chr17:17586800-17587800	Enhancers	Fetal Thymus	thymus
6	chr17:17586800-17588200	Enhancers	Primary B cells from peripheral blood	blood
7	chr17:17586800-17588400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:17586800-17589200	Enhancers	Fetal Lung	lung
9	chr17:17586800-17590600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr17:17586800-17591000	Enhancers	Esophagus	oesophagus
11	chr17:17586800-17591000	Enhancers	Fetal Heart	heart
12	chr17:17587000-17587600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr17:17587000-17587600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr17:17587000-17587600	Enhancers	Adipose Nuclei	Adipose
15	chr17:17587000-17587600	Enhancers	Small Intestine	intestine
16	chr17:17587000-17587800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr17:17587000-17588000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:17587000-17588200	Weak transcription	Gastric	stomach
19	chr17:17587000-17588200	Enhancers	Stomach Smooth Muscle	stomach
20	chr17:17587000-17588400	Weak transcription	Fetal Kidney	kidney
21	chr17:17587000-17588600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:17587000-17589000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:17587000-17589200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:17587000-17589400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr17:17587000-17590400	Enhancers	Fetal Intestine Large	intestine
26	chr17:17587000-17590400	Enhancers	Fetal Muscle Trunk	muscle
27	chr17:17587000-17590600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:17587000-17590800	Enhancers	Left Ventricle	heart
29	chr17:17587000-17591000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:17587000-17591000	Enhancers	Fetal Muscle Leg	muscle
31	chr17:17587000-17591600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr17:17587000-17593000	Weak transcription	Thymus	Thymus
33	chr17:17587200-17587600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:17587200-17587600	Flanking Active TSS	A549	lung
35	chr17:17587200-17587600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr17:17587200-17587800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:17587200-17588000	Enhancers	Dnd41	blood
38	chr17:17587200-17588200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:17587200-17588200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:17587200-17588200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr17:17587200-17588200	Weak transcription	Liver	Liver
42	chr17:17587200-17588200	Weak transcription	Brain Angular Gyrus	brain
43	chr17:17587200-17588200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr17:17587200-17588200	Weak transcription	Brain Germinal Matrix	brain
45	chr17:17587200-17588200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr17:17587200-17588200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:17587200-17588200	Weak transcription	Colonic Mucosa	Colon
48	chr17:17587200-17588200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr17:17587200-17588200	Weak transcription	Lung	lung
50	chr17:17587200-17588200	Weak transcription	Rectal Mucosa Donor 29	rectum

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