Variant report

Variant	rs2316263
Chromosome Location	chr3:99900096-99900097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf26-1	chr3:99898411-99900574	ENSG00000261533.1
2	lnc-C3orf26-1	chr3:99898452-99900574	NONHSAT090862

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1017967	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10222474	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12487143	0.86[CHB][hapmap]
rs12488245	0.80[JPT][hapmap]
rs12629505	0.98[ASN][1000 genomes]
rs16841874	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2130369	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs6767441	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs6776886	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798114	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6810262	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs720688	0.81[ASN][1000 genomes]
rs7623587	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7629487	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7631174	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7653276	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289981	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9290003	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9811920	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MKK][hapmap]
rs9814549	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9837131	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap]
rs9847283	0.92[CEU][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9849632	0.81[ASN][1000 genomes]
rs9849977	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9850382	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9865713	0.81[ASN][1000 genomes]
rs9868170	0.90[AMR][1000 genomes];0.92[EUR][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2316263	SENP7	cis	parietal	SCAN
rs2316263	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs2316263	TMEM45A	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99877600-99904600	Weak transcription	Right Ventricle	heart
2	chr3:99892600-99904200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:99895000-99904600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:99898400-99902400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:99898600-99903800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:99898600-99904200	Weak transcription	Ovary	ovary
7	chr3:99899000-99900400	Weak transcription	Lung	lung
8	chr3:99899000-99902400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:99899000-99902600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:99899000-99903800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:99899000-99904200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:99899000-99904200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:99899000-99904200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:99899000-99907800	Weak transcription	Psoas Muscle	Psoas
15	chr3:99899000-99911000	Weak transcription	Aorta	Aorta
16	chr3:99899200-99902800	Weak transcription	Fetal Stomach	stomach
17	chr3:99899200-99903000	Weak transcription	NHDF-Ad	bronchial
18	chr3:99899200-99903800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:99899200-99904200	Weak transcription	Left Ventricle	heart
20	chr3:99899400-99903200	Weak transcription	Adipose Nuclei	Adipose
21	chr3:99899400-99903600	Weak transcription	Fetal Lung	lung
22	chr3:99899400-99903800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:99899400-99904000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:99899600-99903800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:99899600-99903800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:99899600-99904200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:99899600-99904400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:99899800-99900400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:99899800-99903800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:99900000-99902800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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