Variant report

Variant	rs9997245
Chromosome Location	chr4:166309213-166309214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:166298064..166301679-chr4:166306197..166309667,4	MCF-7	breast:
2	chr4:166304221..166306699-chr4:166307750..166310906,4	MCF-7	breast:
3	chr4:166300805..166303563-chr4:166307690..166309823,2	K562	blood:

Variant related genes	Relation type
ENSG00000109472	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10022413	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10517844	0.83[MEX][hapmap]
rs11100610	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11724810	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732583	0.83[MEX][hapmap]
rs11736871	0.83[MEX][hapmap]
rs13110854	0.92[ASN][1000 genomes]
rs1438109	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17686863	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17686882	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs1866224	0.83[MEX][hapmap]
rs28372351	0.84[ASN][1000 genomes]
rs28503877	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28604413	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28729471	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34405858	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35212926	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35355030	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4691190	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4691191	0.83[ASN][1000 genomes]
rs72701678	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs729699	0.83[MEX][hapmap]
rs9308104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9631752	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9631753	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9631765	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997470	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9997481	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9999764	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9997245	NPY1R	cis	parietal	SCAN
rs9997245	CPE	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166301400-166314800	Weak transcription	Fetal Kidney	kidney
2	chr4:166302200-166314600	Weak transcription	Brain Substantia Nigra	brain
3	chr4:166304000-166311000	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:166304400-166332400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:166305200-166314800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:166305200-166319400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:166305600-166314200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:166305800-166330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:166306400-166309600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:166306400-166314200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:166306600-166324800	Weak transcription	Fetal Stomach	stomach
12	chr4:166307000-166314600	Weak transcription	Fetal Lung	lung
13	chr4:166307200-166322200	Weak transcription	HepG2	liver
14	chr4:166308200-166309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:166308400-166310000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:166308400-166312600	Weak transcription	Fetal Brain Female	brain
17	chr4:166309000-166309400	Enhancers	Aorta	Aorta
18	chr4:166309000-166312200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr4:166309200-166310800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links