Variant report

Variant	rs17666993
Chromosome Location	chr16:72146666-72146667
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:72143268..72145406-chr16:72145794..72147509,2	MCF-7	breast:
2	chr16:72144522..72146740-chr16:72151105..72152934,2	K562	blood:
3	chr16:71879780..71881511-chr16:72144276..72147011,2	MCF-7	breast:
4	chr16:72139817..72142813-chr16:72144026..72146841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140829	Chromatin interaction
ENSG00000224470	Chromatin interaction
ENSG00000182149	Chromatin interaction

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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17667053	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
rs17666993	CRX	trans	brain	seeQTL
rs17666993	TTR	trans	brain	seeQTL
rs17666993	GUCA1C	trans	brain	seeQTL
rs17666993	SH2D2A	trans	brain	seeQTL
rs17666993	SLC5A7	trans	brain	seeQTL
rs17666993	LRTM1	trans	brain	seeQTL

Chromatin state (count:125 , 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	chr16:72129800-72147000	Strong transcription	Ovary	ovary
3	chr16:72129800-72147200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:72129800-72147600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr16:72129800-72147800	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:72129800-72148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:72129800-72149000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:72130000-72146800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr16:72130000-72146800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr16:72130000-72147000	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr16:72130000-72147000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr16:72130000-72147000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr16:72130000-72147000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:72130000-72147000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr16:72130000-72147000	Strong transcription	Esophagus	oesophagus
16	chr16:72130000-72147000	Strong transcription	NHEK	skin
17	chr16:72130000-72147200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:72130000-72147200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:72130000-72147200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr16:72130000-72147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr16:72130000-72147200	Strong transcription	Aorta	Aorta
22	chr16:72130000-72147200	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr16:72130000-72147200	Strong transcription	Brain Substantia Nigra	brain
24	chr16:72130000-72147200	Strong transcription	Fetal Lung	lung
25	chr16:72130000-72147200	Strong transcription	Left Ventricle	heart
26	chr16:72130000-72147400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr16:72130000-72147400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:72130000-72147400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr16:72130000-72147400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr16:72130000-72147400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:72130000-72147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:72130000-72147400	Strong transcription	Adipose Nuclei	Adipose
33	chr16:72130000-72147400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr16:72130000-72147400	Strong transcription	Fetal Brain Female	brain
35	chr16:72130000-72147400	Strong transcription	Fetal Thymus	thymus
36	chr16:72130000-72147400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr16:72130000-72147400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr16:72130000-72147600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr16:72130000-72147600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr16:72130000-72147600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr16:72130000-72147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr16:72130000-72147600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr16:72130000-72147600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr16:72130000-72147600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr16:72130000-72147600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:72130000-72147600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr16:72130000-72147600	Strong transcription	NHLF	lung
48	chr16:72130000-72147800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr16:72130000-72147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr16:72130000-72147800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links