Variant report

Variant	rs10120688
Chromosome Location	chr9:22056499-22056500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTAP-1	chr9:22056247-22056802	NONHSAT130429

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10115049	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10120806	0.90[EUR][1000 genomes]
rs10738605	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10757264	0.94[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs10757265	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10757266	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10757267	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10811640	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10811643	0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10811644	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10811645	0.90[EUR][1000 genomes]
rs10965212	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10965215	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10965219	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1333036	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1360590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1591136	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2106119	0.81[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2106120	0.81[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2151280	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2184061	0.85[ASN][1000 genomes]
rs2383204	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs490005	0.81[ASN][1000 genomes]
rs496892	0.94[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4977753	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504318	0.81[ASN][1000 genomes]
rs567453	0.81[ASN][1000 genomes]
rs643319	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7027048	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027950	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7028570	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7035484	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7044859	0.81[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7049105	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs944799	0.90[EUR][1000 genomes];0.93[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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22052000-22058200	Weak transcription	Primary B cells from cord blood	blood
2	chr9:22052000-22059200	Strong transcription	Dnd41	blood
3	chr9:22053200-22061200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:22053600-22057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:22053800-22057200	Weak transcription	HUVEC	blood vessel
6	chr9:22053800-22058600	Weak transcription	Osteobl	bone
7	chr9:22053800-22059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:22053800-22059800	Weak transcription	HSMM	muscle
9	chr9:22053800-22060000	Weak transcription	NHLF	lung
10	chr9:22053800-22061200	Weak transcription	NHDF-Ad	bronchial
11	chr9:22053800-22061400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:22053800-22065200	Weak transcription	NHEK	skin
13	chr9:22053800-22069000	Weak transcription	Hela-S3	cervix
14	chr9:22053800-22079800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:22054000-22064000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:22055000-22059000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:22055200-22056600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:22055600-22079800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:22056000-22060600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:22056400-22056800	Strong transcription	NH-A	brain
21	chr9:22056400-22057000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:22056400-22058800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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