Variant report

Variant	rs17421460
Chromosome Location	chr9:86326265-86326266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86325511..86327596-chr9:86327772..86330083,2	K562	blood:
2	chr9:86322177..86324075-chr9:86324629..86327063,2	K562	blood:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10124714	0.92[ASN][1000 genomes]
rs1052690	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs11140224	0.92[ASN][1000 genomes]
rs11792478	1.00[CHD][hapmap];0.95[GIH][hapmap]
rs2068465	0.92[ASN][1000 genomes]
rs2542804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2780971	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2780973	0.93[CEU][hapmap];0.84[AMR][1000 genomes]
rs2780976	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2780994	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2781002	1.00[CHD][hapmap]
rs2781004	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2781005	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2781006	1.00[CHD][hapmap]
rs2781007	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2811904	0.84[AMR][1000 genomes]
rs2811910	0.92[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2811913	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2811914	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2811918	0.93[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs41308878	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41309243	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56403955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72746868	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72746869	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72746871	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72746879	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72746880	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72746882	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7866941	0.92[ASN][1000 genomes]
rs9410882	0.93[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17421460	FAM75D5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86324200-86327600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:86324200-86327600	Weak transcription	Brain Substantia Nigra	brain
3	chr9:86324200-86327800	Weak transcription	Brain Anterior Caudate	brain
4	chr9:86324200-86327800	Weak transcription	Brain Hippocampus Middle	brain
5	chr9:86324200-86328200	Weak transcription	Fetal Intestine Small	intestine
6	chr9:86324200-86328800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr9:86324200-86328800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr9:86324200-86329000	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:86324200-86329200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:86324200-86329200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:86324200-86330000	Weak transcription	Primary T cells from cord blood	blood
12	chr9:86324200-86330400	Weak transcription	HSMMtube	muscle
13	chr9:86324200-86331000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:86324200-86331800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:86324400-86327600	Weak transcription	Liver	Liver
16	chr9:86324400-86328000	Weak transcription	Fetal Kidney	kidney
17	chr9:86324400-86328400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:86324600-86328400	Weak transcription	Pancreas	Pancrea
19	chr9:86324600-86329000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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