Variant report

Variant	rs9908168
Chromosome Location	chr17:17223851-17223852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17207665..17210654-chr17:17223210..17225727,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11078383	0.97[ASN][1000 genomes]
rs11078384	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11655849	0.97[ASN][1000 genomes]
rs11869054	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11869079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601631	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12946386	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3785506	0.96[ASN][1000 genomes]
rs4985706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220057	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs758742	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889355	0.97[ASN][1000 genomes]
rs9889834	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9896970	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9904396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs9912599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9914692	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1061186	chr17:17200427-17314406	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9908168	PIGL	cis	parietal	SCAN
rs9908168	COPS3	cis	multi-tissue	Pritchard
rs9908168	RAI1	cis	parietal	SCAN
rs9908168	FLCN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17207400-17235400	Weak transcription	Lung	lung
2	chr17:17207600-17246400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:17207800-17226400	Weak transcription	Brain Angular Gyrus	brain
4	chr17:17207800-17228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:17207800-17228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr17:17207800-17228400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:17207800-17229600	Weak transcription	Adipose Nuclei	Adipose
8	chr17:17207800-17243400	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:17208000-17226000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr17:17208000-17226200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:17208200-17225400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:17208200-17225400	Weak transcription	Brain Anterior Caudate	brain
13	chr17:17208200-17226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:17208200-17228200	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:17208400-17225400	Weak transcription	Brain Germinal Matrix	brain
16	chr17:17208600-17255400	Weak transcription	Brain Substantia Nigra	brain
17	chr17:17208800-17236000	Weak transcription	Right Ventricle	heart
18	chr17:17209000-17226000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:17209000-17227600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr17:17209200-17224000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr17:17209200-17224600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr17:17209800-17226400	Weak transcription	Fetal Intestine Small	intestine
23	chr17:17210600-17233400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:17212400-17229000	Weak transcription	Fetal Brain Male	brain
25	chr17:17213000-17248000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr17:17215400-17229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:17215600-17225800	Weak transcription	Fetal Brain Female	brain
28	chr17:17215600-17226600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:17215600-17226600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr17:17215600-17228000	Weak transcription	Ovary	ovary
31	chr17:17215600-17231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:17215600-17252800	Weak transcription	Fetal Lung	lung
33	chr17:17215800-17228000	Weak transcription	Dnd41	blood
34	chr17:17216600-17240800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:17217000-17229600	Weak transcription	Gastric	stomach
36	chr17:17217000-17231800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:17217200-17224200	Weak transcription	Spleen	Spleen
38	chr17:17217200-17225400	Weak transcription	Fetal Muscle Leg	muscle
39	chr17:17217200-17253800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:17218200-17224600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:17218400-17228000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:17218600-17239800	Weak transcription	Fetal Thymus	thymus
43	chr17:17219000-17225800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr17:17219000-17226000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:17219000-17231400	Weak transcription	K562	blood
46	chr17:17219000-17255400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:17221200-17225600	Weak transcription	Fetal Stomach	stomach
48	chr17:17223600-17224800	Strong transcription	Thymus	Thymus
49	chr17:17223600-17230200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:17223800-17224200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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