Variant report

Variant	rs7864107
Chromosome Location	chr9:3565211-3565212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10114162	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10114838	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10115088	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10115578	0.87[CEU][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap]
rs10118702	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119982	0.87[CEU][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs10121096	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs10758299	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10814189	0.91[JPT][hapmap]
rs10814190	0.90[JPT][hapmap]
rs10814208	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10814219	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10814233	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10814235	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10814250	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814251	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10972435	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10972438	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1133463	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1133467	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12004862	0.87[CEU][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12238307	0.87[CEU][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs12340274	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12353393	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs12684702	0.84[ASN][1000 genomes]
rs1342542	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs2027089	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28510559	0.85[EUR][1000 genomes]
rs3954945	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7022948	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7026025	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7027862	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7041399	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7042747	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7045092	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7847562	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7857554	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7858486	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7861625	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7867083	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871094	0.90[ASN][1000 genomes]
rs7871777	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7873538	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881167	0.87[CEU][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs9774864	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9792451	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3343800	chr9:3559495-3616759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv2762783	chr9:3561910-3618770	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv892092	chr9:3565211-3687942	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7864107	RP11-509J21.1	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3527400-3567600	Weak transcription	Ovary	ovary
2	chr9:3529000-3579000	Weak transcription	HSMMtube	muscle
3	chr9:3531000-3575800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:3531800-3579000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:3547600-3572800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:3549400-3570200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:3549800-3572800	Weak transcription	Right Ventricle	heart
8	chr9:3550000-3566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:3550000-3593000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:3551000-3571200	Weak transcription	Thymus	Thymus
11	chr9:3554400-3576000	Weak transcription	Adipose Nuclei	Adipose
12	chr9:3554400-3576400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:3554400-3579400	Weak transcription	Left Ventricle	heart
14	chr9:3554600-3569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:3554800-3578000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:3560800-3571000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:3560800-3571400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:3562800-3568000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:3563200-3565400	Weak transcription	Lung	lung
20	chr9:3563600-3566000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:3563800-3566000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr9:3563800-3567200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:3563800-3576200	Weak transcription	Primary B cells from cord blood	blood
24	chr9:3563800-3578200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:3565200-3568400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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