Variant report

Variant	rs10965219
Chromosome Location	chr9:22053687-22053688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:22051930..22054348-chr9:22086021..22088331,2	MCF-7	breast:
2	chr9:22051697..22054295-chr9:22107294..22109558,2	MCF-7	breast:
3	chr9:22051314..22055495-chr9:22237121..22240202,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTAP-1	chr9:22051172-22054011	NONHSAT130430

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10115049	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10120688	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10120806	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10738605	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757263	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10757264	0.81[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs10757265	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757266	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757267	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811640	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811643	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811644	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10811645	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10965212	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10965215	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1333035	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1333036	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360590	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591136	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2106119	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2106120	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2151280	0.89[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2184061	0.81[ASN][1000 genomes]
rs2383204	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811712	0.81[YRI][hapmap]
rs3218002	0.81[YRI][hapmap]
rs3218005	0.81[YRI][hapmap]
rs490005	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs496892	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4977753	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs504318	0.81[CEU][hapmap];0.87[ASN][1000 genomes]
rs567453	0.87[ASN][1000 genomes]
rs581876	0.80[ASN][1000 genomes]
rs643319	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7027048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027950	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028570	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035484	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7044859	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7049105	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs944799	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs10965219	RRAGA	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22049200-22053800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:22049400-22053800	Enhancers	HUVEC	blood vessel
3	chr9:22049400-22054000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:22050200-22053800	Enhancers	NHEK	skin
5	chr9:22050400-22053800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:22050600-22053800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:22051200-22055600	Weak transcription	Esophagus	oesophagus
8	chr9:22051800-22053800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:22051800-22053800	Enhancers	HSMM	muscle
10	chr9:22051800-22054000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:22051800-22054000	Enhancers	HMEC	breast
12	chr9:22051800-22056000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr9:22052000-22053800	Enhancers	Hela-S3	cervix
14	chr9:22052000-22053800	Enhancers	Osteobl	bone
15	chr9:22052000-22054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:22052000-22058200	Weak transcription	Primary B cells from cord blood	blood
17	chr9:22052000-22059200	Strong transcription	Dnd41	blood
18	chr9:22052200-22053800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:22052200-22053800	Enhancers	NHDF-Ad	bronchial
20	chr9:22052200-22053800	Enhancers	NHLF	lung
21	chr9:22052400-22054200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:22052400-22054400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:22053000-22055400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:22053200-22055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:22053200-22061200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:22053400-22054000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr9:22053600-22053800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:22053600-22054600	Enhancers	NH-A	brain
29	chr9:22053600-22055200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:22053600-22055200	Weak transcription	HSMMtube	muscle
31	chr9:22053600-22057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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