Variant report

Variant	rs166815
Chromosome Location	chr10:49459610-49459611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN20C-7	chr10:49459609-49459654	NONHSAT013263

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11816450	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12246849	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12262288	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1465605	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1652243	1.00[ASN][1000 genomes]
rs1652245	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs166817	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009533	1.00[JPT][hapmap]
rs1730444	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1730445	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1730446	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1881733	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1881734	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs204006	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2455321	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2463958	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652408	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2698763	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2698764	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280605	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280606	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs280608	1.00[ASW][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280610	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280611	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs280615	0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs280617	1.00[AMR][1000 genomes]
rs386570	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs399419	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs413065	1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426153	1.00[ASN][1000 genomes]
rs432971	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs440894	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs440943	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs477693	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs477761	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57211602	1.00[AMR][1000 genomes]
rs572211	0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57415323	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59368050	0.83[AMR][1000 genomes]
rs60503953	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61840508	1.00[ASN][1000 genomes]
rs7068083	1.00[AMR][1000 genomes]
rs7068262	1.00[AMR][1000 genomes]
rs7069773	0.83[AMR][1000 genomes]
rs7073154	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7092864	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73294264	1.00[ASN][1000 genomes]
rs73296347	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73296348	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73296379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296380	1.00[ASN][1000 genomes]
rs73296381	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73296382	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296386	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73296387	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7915333	1.00[JPT][hapmap];1.00[ASN][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	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv895370	chr10:49421173-49484698	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49457000-49460800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:49458200-49460800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:49458400-49464000	Weak transcription	Right Atrium	heart
4	chr10:49458800-49460800	Enhancers	Fetal Thymus	thymus
5	chr10:49458800-49463600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:49459000-49460400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr10:49459000-49460800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:49459000-49460800	Enhancers	Esophagus	oesophagus
9	chr10:49459000-49461400	Enhancers	Fetal Heart	heart
10	chr10:49459000-49463600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:49459000-49463600	Enhancers	HMEC	breast
12	chr10:49459200-49459800	Enhancers	Brain Hippocampus Middle	brain
13	chr10:49459200-49459800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr10:49459200-49460000	Flanking Active TSS	HepG2	liver
15	chr10:49459200-49460400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr10:49459200-49460400	Enhancers	Fetal Kidney	kidney
17	chr10:49459200-49460400	Enhancers	Gastric	stomach
18	chr10:49459200-49460600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:49459200-49460800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr10:49459200-49460800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:49459200-49460800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:49459200-49460800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr10:49459200-49460800	Enhancers	Pancreas	Pancrea
24	chr10:49459200-49461000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:49459200-49461000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:49459200-49462200	Enhancers	NHEK	skin
27	chr10:49459400-49459800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:49459400-49459800	Enhancers	Brain Substantia Nigra	brain
29	chr10:49459400-49459800	Enhancers	A549	lung
30	chr10:49459400-49459800	Enhancers	GM12878-XiMat	blood
31	chr10:49459400-49460000	Enhancers	Right Ventricle	heart
32	chr10:49459400-49460000	Enhancers	Hela-S3	cervix
33	chr10:49459400-49460600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:49459400-49460600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr10:49459400-49460600	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr10:49459400-49460800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:49459400-49460800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr10:49459400-49460800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr10:49459400-49460800	Enhancers	Left Ventricle	heart
40	chr10:49459400-49461000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr10:49459600-49460000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr10:49459600-49460000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:49459600-49461000	Enhancers	HUES64 Cell Line	embryonic stem cell

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