Variant report

Variant	rs10965215
Chromosome Location	chr9:22029445-22029446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:24)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21991860..21994281-chr9:22027750..22030080,2	MCF-7	breast:
2	chr9:22006075..22010521-chr9:22028543..22032768,5	MCF-7	breast:

(count:24 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
2	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
3	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
4	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
5	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
6	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
7	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
8	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
9	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
10	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
11	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
12	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
13	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
14	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
15	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
16	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
17	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
18	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
19	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
20	lnc-MTAP-1	chr9:22029432-22029593	ENSG00000240498.2
21	lnc-MTAP-1	chr9:22029432-22029593	NONHSAT130421
22	lnc-MTAP-1	chr9:22029432-22029593	NONHSAT130429
23	lnc-MTAP-1	chr9:22029432-22029593	NR_003529
24	lnc-MTAP-1	chr9:22029432-22029593	NONHSAT130426

No data

Variant related genes	Relation type
ENSG00000147883	Chromatin interaction
TMEM258	LncRNA region
ADIPOR1	LncRNA region
VAMP3	LncRNA region
CARD8	LncRNA region
CDKN2B	LncRNA region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10115049	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120688	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10120806	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10738605	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757263	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757264	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757265	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757266	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10757267	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811640	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811645	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10965212	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10965219	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1333036	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1360590	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1591136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106119	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106120	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151280	0.88[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2383204	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2518723	0.82[AMR][1000 genomes]
rs3218012	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490005	1.00[ASN][1000 genomes]
rs496892	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4977753	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504318	0.85[CEU][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567453	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581876	0.90[ASN][1000 genomes]
rs643319	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027048	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7027950	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7028570	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7035484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044859	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7049105	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944799	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10965215	RRAGA	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22009800-22030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:22009800-22037000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:22010000-22029800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:22022800-22032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:22025000-22033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:22025400-22039800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:22028800-22030400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr9:22029000-22032400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr9:22029200-22030400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:22029200-22031800	Strong transcription	Dnd41	blood
11	chr9:22029400-22029600	Flanking Active TSS	GM12878-XiMat	blood
12	chr9:22029400-22030200	Enhancers	Primary B cells from cord blood	blood
13	chr9:22029400-22030400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:22029400-22030400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:22029400-22030400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr9:22029400-22030600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:22029400-22030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:22029400-22030800	Enhancers	NHDF-Ad	bronchial
19	chr9:22029400-22031000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:22029400-22031000	Enhancers	Hela-S3	cervix
21	chr9:22029400-22031000	Enhancers	HUVEC	blood vessel
22	chr9:22029400-22032600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:22029400-22034200	Enhancers	HMEC	breast

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