Variant report

Variant	rs4478644
Chromosome Location	chr9:86005599-86005600
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85997879..86001519-chr9:86002024..86006738,6	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10117284	0.93[ASW][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10125072	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140060	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12349789	0.93[ASW][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13299648	0.91[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28585601	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3849865	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3860901	0.88[GIH][hapmap];0.90[TSI][hapmap]
rs3860905	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3860906	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860907	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860909	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860912	0.86[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3860913	0.89[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3860914	0.95[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3904187	0.86[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3904189	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4297106	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4877756	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs4877757	0.95[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7019165	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037795	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7037928	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4478644	TLE1	cis	parietal	SCAN
rs4478644	C9orf64	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85958200-86007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:85998800-86008600	Weak transcription	Pancreas	Pancrea
3	chr9:85999400-86008400	Weak transcription	Aorta	Aorta
4	chr9:86000000-86005800	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:86000000-86006600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:86000000-86020600	Weak transcription	Fetal Brain Female	brain
7	chr9:86000400-86005600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr9:86003400-86006600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:86004600-86014200	Weak transcription	Gastric	stomach
10	chr9:86004800-86005800	Weak transcription	Left Ventricle	heart
11	chr9:86005000-86006800	Weak transcription	HepG2	liver
12	chr9:86005200-86006400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:86005400-86006600	Weak transcription	Psoas Muscle	Psoas
14	chr9:86005400-86006600	Weak transcription	Spleen	Spleen
15	chr9:86005400-86021000	Weak transcription	Right Atrium	heart

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