Variant report

Variant	rs999953
Chromosome Location	chr5:146956448-146956449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:146603532..146604750-chr5:146956351..146957631,4	MCF-7	breast:
2	chr5:146956209..146957226-chr5:147202038..147202593,3	MCF-7	breast:
3	chr5:146832995..146833970-chr5:146956353..146957177,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113657	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10045944	0.98[EUR][1000 genomes]
rs10051794	0.98[EUR][1000 genomes]
rs10515588	0.89[EUR][1000 genomes]
rs1106895	0.86[EUR][1000 genomes]
rs1159523	0.86[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1347138	0.85[EUR][1000 genomes]
rs1529685	0.87[EUR][1000 genomes]
rs1529686	0.87[EUR][1000 genomes]
rs1529687	0.87[EUR][1000 genomes]
rs1529688	0.87[EUR][1000 genomes]
rs17096666	0.87[EUR][1000 genomes]
rs17106902	0.89[ASN][1000 genomes]
rs17106906	0.89[ASN][1000 genomes]
rs17106940	0.97[EUR][1000 genomes]
rs17106947	0.97[EUR][1000 genomes]
rs17106977	0.90[EUR][1000 genomes]
rs17106994	0.87[EUR][1000 genomes]
rs17106995	0.87[EUR][1000 genomes]
rs17107039	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs17107043	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2116765	0.93[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2116768	0.90[EUR][1000 genomes]
rs2116769	0.90[EUR][1000 genomes]
rs2304036	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs34100034	0.88[EUR][1000 genomes]
rs35502493	0.99[EUR][1000 genomes]
rs3763093	0.97[EUR][1000 genomes]
rs3763094	0.97[EUR][1000 genomes]
rs3765006	0.87[EUR][1000 genomes]
rs4382156	0.87[EUR][1000 genomes]
rs4382157	0.87[EUR][1000 genomes]
rs4577681	0.85[EUR][1000 genomes]
rs4635925	0.89[EUR][1000 genomes]
rs4705176	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4705181	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55851807	0.97[EUR][1000 genomes]
rs56295956	0.97[EUR][1000 genomes]
rs56384964	0.98[EUR][1000 genomes]
rs57061855	0.87[EUR][1000 genomes]
rs58595614	0.97[EUR][1000 genomes]
rs59225792	0.87[EUR][1000 genomes]
rs61508445	0.89[EUR][1000 genomes]
rs6580478	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6580480	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6860404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6887481	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs6892958	0.96[EUR][1000 genomes]
rs73268153	0.87[EUR][1000 genomes]
rs73268172	0.87[EUR][1000 genomes]
rs7380570	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7704474	0.98[EUR][1000 genomes]
rs7705148	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7706575	0.86[EUR][1000 genomes]
rs7711029	0.97[EUR][1000 genomes]
rs7711042	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7725758	0.87[EUR][1000 genomes]
rs7729949	0.87[EUR][1000 genomes]
rs8180519	0.97[EUR][1000 genomes]
rs8180520	0.88[EUR][1000 genomes]
rs9325047	0.89[EUR][1000 genomes]
rs9686194	0.88[EUR][1000 genomes]
rs9686196	0.88[EUR][1000 genomes]
rs9686961	0.87[EUR][1000 genomes]
rs981644	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9918128	0.87[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs999953	JAKMIP2	cis	parietal	SCAN
rs999953	CSF1R	cis	cerebellum	SCAN
rs999953	CAMK2A	cis	cerebellum	SCAN
rs999953	UQCC	trans	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146945600-146957400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:146946800-146956800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:146954600-146956800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:146954600-146956800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:146954600-146956800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:146954600-146957200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:146954600-146974000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:146954800-146956800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:146954800-146956800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:146954800-146956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:146954800-146956800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:146954800-146957800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:146954800-146973800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:146955000-146956800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:146955000-146956800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:146955000-146956800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:146955000-146956800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:146955000-146956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:146955200-146956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:146956200-146957000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:146956200-146957000	Enhancers	Ovary	ovary
22	chr5:146956200-146958000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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