Variant report

Variant	rs2686206
Chromosome Location	chr8:11620315-11620316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11618295..11620623-chr8:11664020..11665628,2	K562	blood:
2	chr8:11619764..11620442-chr8:11816053..11817012,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf49-1	chr8:11618765-11620732	NONHSAT125071
2	lnc-C8orf49-1	chr8:11619626-11620425	NONHSAT147620

Variant related genes	Relation type
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1004712	0.86[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10108052	0.81[ASN][1000 genomes]
rs10108876	0.81[ASN][1000 genomes]
rs1062219	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs11778526	0.81[ASN][1000 genomes]
rs12458	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1466785	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2645453	0.84[ASN][1000 genomes]
rs2740433	0.88[ASN][1000 genomes]
rs7015453	0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs804276	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs867858	0.87[JPT][hapmap]
rs9329248	0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs9644752	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2686206	SGCZ	cis	cerebellum	SCAN
rs2686206	TUSC3	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11607000-11622800	Weak transcription	Stomach Mucosa	stomach
2	chr8:11610600-11621200	Strong transcription	Fetal Intestine Small	intestine
3	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
4	chr8:11617000-11622800	Weak transcription	Fetal Heart	heart
5	chr8:11617000-11623000	Weak transcription	Placenta	Placenta
6	chr8:11617000-11626800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:11617400-11622800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:11617400-11623200	Weak transcription	HepG2	liver
9	chr8:11617400-11626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:11617400-11626400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:11617400-11626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:11618000-11626000	Weak transcription	Pancreas	Pancrea
13	chr8:11618000-11626800	Weak transcription	Fetal Intestine Large	intestine
14	chr8:11618400-11623000	Weak transcription	Liver	Liver
15	chr8:11618800-11620800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:11619000-11621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:11619200-11620400	Enhancers	Right Ventricle	heart
18	chr8:11619200-11620400	Enhancers	HMEC	breast
19	chr8:11619200-11620400	Enhancers	NHLF	lung
20	chr8:11619200-11620600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr8:11619200-11621000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:11619400-11620400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:11619400-11620400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:11619400-11620400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:11619400-11620400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr8:11619400-11620400	Enhancers	HSMM	muscle
27	chr8:11619400-11620400	Enhancers	HSMMtube	muscle
28	chr8:11619400-11620400	Flanking Active TSS	NH-A	brain
29	chr8:11619400-11620600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:11619400-11620800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:11619600-11620400	Flanking Active TSS	HUVEC	blood vessel
32	chr8:11619600-11620400	Flanking Active TSS	Osteobl	bone
33	chr8:11619600-11622000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr8:11619600-11623200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:11619600-11623200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr8:11619600-11623200	Weak transcription	Primary B cells from cord blood	blood
37	chr8:11619600-11626800	Weak transcription	Gastric	stomach
38	chr8:11619800-11620400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr8:11619800-11620400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr8:11620000-11620400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr8:11620000-11620400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr8:11620000-11620400	Flanking Active TSS	A549	lung
43	chr8:11620000-11620400	Bivalent Enhancer	Hela-S3	cervix
44	chr8:11620000-11620400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr8:11620000-11620400	Flanking Active TSS	NHEK	skin
46	chr8:11620200-11620400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:11620200-11620400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr8:11620200-11620400	Enhancers	K562	blood
49	chr8:11620200-11620600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:11620200-11620600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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