Variant report

Variant	rs9895806
Chromosome Location	chr17:19675547-19675548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ULK2-2	chr17:19674142-19677237	NONHSAT146527

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12103837	1.00[AMR][1000 genomes]
rs16960425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16960503	0.84[ASW][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.82[AFR][1000 genomes]
rs28416178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491526	0.95[AFR][1000 genomes]
rs28632080	0.81[AFR][1000 genomes]
rs8064668	0.89[AFR][1000 genomes]
rs8064945	1.00[AMR][1000 genomes]
rs8072354	1.00[AMR][1000 genomes]
rs9889660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893138	0.82[AFR][1000 genomes]
rs9897053	1.00[AMR][1000 genomes]
rs9905439	1.00[AMR][1000 genomes]
rs9905570	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9906047	1.00[AFR][1000 genomes]
rs9906125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9906263	0.89[AFR][1000 genomes]
rs9910607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9912443	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9913673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9914597	1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9914797	1.00[AMR][1000 genomes]
rs9915262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9915902	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9916309	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1061489	chr17:19654704-19705026	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19666000-19676400	Weak transcription	Fetal Intestine Large	intestine
2	chr17:19666000-19676800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:19666000-19676800	Weak transcription	Fetal Lung	lung
4	chr17:19666000-19677000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr17:19666000-19678200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:19666000-19678600	Weak transcription	Left Ventricle	heart
7	chr17:19666000-19678800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:19666000-19679200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:19666000-19691200	Weak transcription	Spleen	Spleen
10	chr17:19666000-19691800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:19666200-19676800	Weak transcription	Gastric	stomach
12	chr17:19669600-19677800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr17:19670200-19677000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:19670200-19678400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:19670200-19679200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:19670200-19679400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:19670200-19694200	Weak transcription	Right Ventricle	heart
18	chr17:19670200-19699400	Weak transcription	Psoas Muscle	Psoas
19	chr17:19670400-19678200	Weak transcription	Placenta	Placenta
20	chr17:19670400-19679000	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:19670400-19683800	Weak transcription	Fetal Brain Male	brain
22	chr17:19670600-19677200	Weak transcription	Liver	Liver
23	chr17:19670600-19678000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr17:19670600-19679200	Weak transcription	Pancreas	Pancrea
25	chr17:19670600-19679200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:19672000-19676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:19672000-19679000	Weak transcription	Ovary	ovary
28	chr17:19672000-19679200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:19672200-19679200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr17:19672600-19678800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:19672800-19675600	Enhancers	GM12878-XiMat	blood
32	chr17:19672800-19676800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr17:19672800-19676800	Strong transcription	Brain Germinal Matrix	brain
34	chr17:19673200-19676400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:19673400-19675600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:19673400-19682200	Strong transcription	Fetal Brain Female	brain
37	chr17:19673600-19675600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:19673600-19677000	Weak transcription	NHEK	skin
39	chr17:19673600-19677200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr17:19673600-19677400	Strong transcription	Fetal Stomach	stomach
41	chr17:19673800-19675600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr17:19673800-19676400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:19673800-19676600	Strong transcription	Fetal Intestine Small	intestine
44	chr17:19673800-19677400	Strong transcription	Lung	lung
45	chr17:19673800-19677800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:19673800-19678400	Weak transcription	Fetal Kidney	kidney
47	chr17:19673800-19679200	Weak transcription	NHLF	lung
48	chr17:19673800-19680200	Weak transcription	HUVEC	blood vessel
49	chr17:19673800-19685000	Weak transcription	HSMM	muscle
50	chr17:19673800-19769800	Weak transcription	NH-A	brain

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