Variant report

Variant	rs2164864
Chromosome Location	chr4:166324427-166324428
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	chr4:166298755..166301718-chr4:166324143..166325651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109472	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10015323	0.82[AMR][1000 genomes]
rs10222703	0.82[ASN][1000 genomes]
rs1370690	0.81[JPT][hapmap]
rs1438114	0.81[GIH][hapmap]
rs1543915	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17624928	0.84[AMR][1000 genomes]
rs2241812	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241813	0.82[AMR][1000 genomes]
rs2241815	0.82[AMR][1000 genomes]
rs2322291	0.83[CHB][hapmap]
rs4308333	0.83[CHB][hapmap]
rs4691193	0.82[AMR][1000 genomes]
rs6810964	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs6833833	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6837454	0.82[AMR][1000 genomes]
rs6837954	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs6848504	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6849361	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7654329	0.85[CEU][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs7699011	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs934819	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2164864	NAF1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166304400-166332400	Weak transcription	Brain Angular Gyrus	brain
2	chr4:166305800-166330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:166306600-166324800	Weak transcription	Fetal Stomach	stomach
4	chr4:166311400-166327400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:166315000-166325200	Weak transcription	Aorta	Aorta
6	chr4:166315800-166328000	Weak transcription	Ovary	ovary
7	chr4:166315800-166332600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:166318200-166330600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:166319200-166332000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:166319600-166361800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:166320000-166339000	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:166320000-166339200	Weak transcription	Brain Substantia Nigra	brain
13	chr4:166320200-166325200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:166320200-166325600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:166320200-166332600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:166322800-166327000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:166323000-166325600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:166323200-166326000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:166323400-166325800	Enhancers	Fetal Brain Male	brain
20	chr4:166323400-166326200	Strong transcription	HepG2	liver
21	chr4:166323600-166325200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:166323600-166330000	Weak transcription	Brain Anterior Caudate	brain
23	chr4:166323800-166325200	Enhancers	Fetal Brain Female	brain
24	chr4:166323800-166325400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:166323800-166325600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:166324400-166326800	Weak transcription	Fetal Intestine Small	intestine

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