Variant report

Variant	rs10982549
Chromosome Location	chr9:117889530-117889531
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNC-1	chr9:117889229-117889906	XLOC_007834

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10119915	1.00[JPT][hapmap]
rs10120799	1.00[JPT][hapmap]
rs10122188	1.00[JPT][hapmap]
rs10125919	1.00[JPT][hapmap]
rs10465131	0.98[ASN][1000 genomes]
rs10817719	1.00[JPT][hapmap]
rs10817720	1.00[JPT][hapmap]
rs10817726	1.00[JPT][hapmap]
rs10982548	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10982551	0.98[ASN][1000 genomes]
rs10982560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982561	0.81[ASN][1000 genomes]
rs10982562	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10982563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982566	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982573	1.00[ASN][1000 genomes]
rs10982574	1.00[ASN][1000 genomes]
rs10982575	1.00[ASN][1000 genomes]
rs10982580	1.00[ASN][1000 genomes]
rs10982581	1.00[ASN][1000 genomes]
rs10982582	1.00[ASN][1000 genomes]
rs10982583	0.98[ASN][1000 genomes]
rs10982584	1.00[ASN][1000 genomes]
rs10982585	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10982586	1.00[ASN][1000 genomes]
rs10982588	1.00[ASN][1000 genomes]
rs10982589	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10982590	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10982591	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10982597	1.00[JPT][hapmap]
rs10982610	1.00[JPT][hapmap]
rs12235377	1.00[JPT][hapmap]
rs12237691	1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12338815	1.00[ASN][1000 genomes]
rs12338911	1.00[ASN][1000 genomes]
rs12347993	1.00[ASN][1000 genomes]
rs12348952	1.00[ASN][1000 genomes]
rs1335331	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes]
rs16932289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932349	1.00[JPT][hapmap]
rs56791225	0.98[ASN][1000 genomes]
rs59205962	0.95[ASN][1000 genomes]
rs60003319	0.95[ASN][1000 genomes]
rs60760004	0.98[ASN][1000 genomes]
rs6478135	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6478136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478138	1.00[ASN][1000 genomes]
rs6478139	1.00[ASN][1000 genomes]
rs6478140	1.00[ASN][1000 genomes]
rs6478141	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6478142	1.00[ASN][1000 genomes]
rs6478144	1.00[ASN][1000 genomes]
rs7021343	0.88[AFR][1000 genomes]
rs7027235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7027851	0.98[ASN][1000 genomes]
rs7031730	1.00[ASN][1000 genomes]
rs7033388	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap]
rs7049043	0.88[AFR][1000 genomes]
rs7847093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7851019	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7851086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7851110	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7851481	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862558	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7864609	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9886855	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117884000-117892600	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:117888800-117889600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:117888800-117889800	Enhancers	Fetal Muscle Leg	muscle
4	chr9:117888800-117890000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:117888800-117890200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:117888800-117890200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:117888800-117890400	Enhancers	HSMM	muscle
8	chr9:117888800-117890400	Enhancers	HSMMtube	muscle
9	chr9:117888800-117890400	Enhancers	NH-A	brain
10	chr9:117888800-117890400	Enhancers	NHLF	lung
11	chr9:117888800-117890400	Enhancers	Osteobl	bone
12	chr9:117888800-117890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:117889000-117889800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:117889000-117890200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:117889000-117890400	Enhancers	NHDF-Ad	bronchial
16	chr9:117889200-117890200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:117889200-117890200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:117889200-117890400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:117889200-117890400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:117889200-117890400	Enhancers	Esophagus	oesophagus
21	chr9:117889200-117890400	Enhancers	HMEC	breast
22	chr9:117889200-117890400	Enhancers	NHEK	skin
23	chr9:117889400-117889800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:117889400-117890400	Enhancers	Fetal Intestine Small	intestine
25	chr9:117889400-117895000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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