Variant report

Variant	rs1883393
Chromosome Location	chr6:25297497-25297498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCGN-4	chr6:25297378-25298038	NONHSAT108152

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12055697	1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs16890366	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs16890377	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2143023	0.87[ASN][1000 genomes]
rs2690042	0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2690111	0.83[CHB][hapmap]
rs2744287	0.95[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4712904	0.98[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4712905	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4712906	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs4712907	0.94[ASN][1000 genomes]
rs55967593	0.87[ASN][1000 genomes]
rs55999195	0.85[ASN][1000 genomes]
rs58191968	0.92[ASN][1000 genomes]
rs60084615	0.92[ASN][1000 genomes]
rs6456664	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6456665	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6456666	0.94[ASN][1000 genomes]
rs6456668	0.84[ASN][1000 genomes]
rs6903148	0.94[ASN][1000 genomes]
rs6906812	0.85[ASN][1000 genomes]
rs6908260	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs6913606	0.94[ASN][1000 genomes]
rs6913886	0.94[ASN][1000 genomes]
rs6914439	0.89[ASN][1000 genomes]
rs6914514	0.94[ASN][1000 genomes]
rs6914654	0.89[ASN][1000 genomes]
rs6914798	0.94[ASN][1000 genomes]
rs6914930	0.94[ASN][1000 genomes]
rs6915270	0.92[ASN][1000 genomes]
rs6917631	0.92[ASN][1000 genomes]
rs6921343	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6923529	0.94[ASN][1000 genomes]
rs6927238	0.83[ASN][1000 genomes]
rs6932783	0.94[EUR][1000 genomes]
rs6938281	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6938594	0.86[JPT][hapmap]
rs730711	0.94[ASN][1000 genomes]
rs73392399	0.94[ASN][1000 genomes]
rs73396126	0.92[ASN][1000 genomes]
rs7741580	0.85[ASN][1000 genomes]
rs7743750	0.94[ASN][1000 genomes]
rs7746942	0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7746969	0.94[ASN][1000 genomes]
rs7755701	0.94[ASN][1000 genomes]
rs7756143	0.94[ASN][1000 genomes]
rs7758529	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs7759796	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7759879	0.85[ASN][1000 genomes]
rs7760067	0.87[ASN][1000 genomes]
rs7760151	0.87[ASN][1000 genomes]
rs7764111	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9295654	0.98[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9348671	0.92[ASN][1000 genomes]
rs9356974	0.94[ASN][1000 genomes]
rs9356975	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs9366615	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs9366616	0.94[ASN][1000 genomes]
rs9379752	0.94[ASN][1000 genomes]
rs9379753	0.91[ASN][1000 genomes]
rs9393639	0.87[ASN][1000 genomes]
rs9393640	0.90[EUR][1000 genomes]
rs9461132	0.94[ASN][1000 genomes]
rs9461134	0.94[ASN][1000 genomes]
rs9461135	0.94[ASN][1000 genomes]
rs9461136	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9467466	0.98[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs999039	0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[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	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:25289000-25298600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:25289000-25300600	Weak transcription	Pancreas	Pancrea
6	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:25292400-25301000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:25293000-25301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:25293200-25301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:25293800-25298000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:25294200-25311200	Weak transcription	Lung	lung
13	chr6:25294600-25297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:25294600-25301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:25295000-25297800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:25295600-25297600	Enhancers	NHLF	lung
17	chr6:25295600-25299400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:25295800-25297800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:25295800-25297800	Enhancers	Thymus	Thymus
20	chr6:25295800-25298000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:25295800-25298000	Enhancers	Fetal Intestine Small	intestine
22	chr6:25295800-25298000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:25295800-25298000	Enhancers	Small Intestine	intestine
24	chr6:25295800-25298000	Enhancers	NHDF-Ad	bronchial
25	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:25295800-25298200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25295800-25298200	Enhancers	Fetal Heart	heart
28	chr6:25295800-25298200	Enhancers	HSMMtube	muscle
29	chr6:25295800-25299200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:25296000-25297600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:25296000-25297600	Enhancers	Aorta	Aorta
32	chr6:25296000-25297800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:25296000-25297800	Enhancers	Fetal Thymus	thymus
34	chr6:25296000-25298000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:25296000-25299200	Enhancers	Fetal Lung	lung
36	chr6:25296000-25301200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:25296200-25297600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:25296400-25298000	Enhancers	Ovary	ovary
39	chr6:25296400-25298000	Enhancers	Stomach Mucosa	stomach
40	chr6:25296400-25298200	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:25296400-25302400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:25296600-25297600	Weak transcription	Brain Angular Gyrus	brain
43	chr6:25296600-25298000	Enhancers	Fetal Stomach	stomach
44	chr6:25296600-25298000	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:25296600-25298200	Enhancers	Fetal Kidney	kidney
46	chr6:25296600-25301200	Weak transcription	Brain Substantia Nigra	brain
47	chr6:25296600-25302400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:25296600-25302600	Weak transcription	Colonic Mucosa	Colon
49	chr6:25296800-25301800	Weak transcription	Fetal Intestine Large	intestine
50	chr6:25296800-25302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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