Variant report

Variant	rs17667053
Chromosome Location	chr16:72147431-72147432
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72143268..72145406-chr16:72145794..72147509,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17603662	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17604185	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17604403	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17604479	0.92[EUR][1000 genomes]
rs17604577	0.92[EUR][1000 genomes]
rs17666927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17666993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2042439	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3815192	1.00[ASW][hapmap]
rs55673524	0.92[EUR][1000 genomes]
rs56030533	1.00[EUR][1000 genomes]
rs56336518	0.92[EUR][1000 genomes]
rs599831	1.00[AMR][1000 genomes];1.00[EUR][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	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	89 gene(s)	inside rSNPs	diseases
2	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
7	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17667053	TTR	trans	brain	seeQTL
rs17667053	SLC5A7	trans	brain	seeQTL
rs17667053	SH2D2A	trans	brain	seeQTL
rs17667053	CRX	trans	brain	seeQTL
rs17667053	GUCA1C	trans	brain	seeQTL
rs17667053	LRTM1	trans	brain	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72129400-72147800	Strong transcription	Primary T cells from cord blood	blood
2	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:72130000-72147600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr16:72130000-72147600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr16:72130000-72147600	Strong transcription	Primary hematopoietic stem cells	blood
9	chr16:72130000-72147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:72130000-72147600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr16:72130000-72147600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr16:72130000-72147600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:72130000-72147600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:72130000-72147600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr16:72130000-72147600	Strong transcription	NHLF	lung
16	chr16:72130000-72147800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr16:72130000-72147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:72130000-72147800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:72130000-72147800	Strong transcription	Brain Anterior Caudate	brain
20	chr16:72130000-72147800	Strong transcription	Brain Hippocampus Middle	brain
21	chr16:72130000-72147800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:72130000-72147800	Strong transcription	Fetal Stomach	stomach
23	chr16:72130000-72147800	Strong transcription	Thymus	Thymus
24	chr16:72130000-72147800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr16:72130000-72148000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr16:72130000-72148000	Strong transcription	Brain Cingulate Gyrus	brain
27	chr16:72130000-72148200	Strong transcription	Liver	Liver
28	chr16:72130000-72148200	Strong transcription	Placenta	Placenta
29	chr16:72130200-72147600	Strong transcription	Colonic Mucosa	Colon
30	chr16:72130200-72147600	Strong transcription	Lung	lung
31	chr16:72130200-72147600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr16:72130200-72147800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:72130200-72147800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr16:72130200-72148000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr16:72130400-72147600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr16:72130400-72147600	Strong transcription	Gastric	stomach
37	chr16:72130800-72148000	Strong transcription	Brain Germinal Matrix	brain
38	chr16:72134600-72147800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr16:72135600-72148400	Strong transcription	Fetal Muscle Leg	muscle
40	chr16:72136200-72148200	Strong transcription	Primary B cells from cord blood	blood
41	chr16:72136400-72148600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr16:72142800-72158600	Weak transcription	Fetal Brain Male	brain
43	chr16:72143000-72147600	Weak transcription	NHDF-Ad	bronchial
44	chr16:72143000-72152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr16:72145400-72147600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:72145600-72147800	Strong transcription	Fetal Intestine Small	intestine
47	chr16:72145800-72150000	Weak transcription	K562	blood
48	chr16:72145800-72150200	Weak transcription	Osteobl	bone
49	chr16:72145800-72152600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr16:72145800-72156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links