Variant report

Variant	rs9916483
Chromosome Location	chr17:34010500-34010501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GAS2L2-1	chr17:34010123-34011922	ENSG00000245181
2	lnc-GAS2L2-1	chr17:34010128-34011922	ENSG00000267003.1

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1037591	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs10491114	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10491115	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11870399	0.92[ASN][1000 genomes]
rs11870475	0.84[ASN][1000 genomes]
rs12449919	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450039	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452633	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12452961	0.92[ASN][1000 genomes]
rs12600662	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12603142	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16971122	0.91[JPT][hapmap]
rs1964509	0.84[ASN][1000 genomes]
rs2079924	0.86[EUR][1000 genomes]
rs226424	0.86[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs226427	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226433	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226435	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226436	0.86[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226437	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278950	0.86[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs2301731	0.92[ASN][1000 genomes]
rs2428463	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523115	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384428	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs28384429	0.92[ASN][1000 genomes]
rs28661650	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3760325	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785759	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs3785763	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62079728	0.92[ASN][1000 genomes]
rs7211363	0.84[ASN][1000 genomes]
rs7213022	0.91[AFR][1000 genomes]
rs9303689	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs9891317	0.92[ASN][1000 genomes]
rs9904644	0.86[ASW][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs9904957	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9906037	0.92[ASN][1000 genomes]
rs9914730	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr17:33960000-34024600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr17:33979400-34016600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:33992800-34028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:33994800-34010600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:33995800-34024600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:33996000-34010800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:33997400-34023200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:33997600-34024600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
15	chr17:33999600-34018200	Weak transcription	Fetal Kidney	kidney
16	chr17:33999800-34010600	Weak transcription	Psoas Muscle	Psoas
17	chr17:34000000-34014200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr17:34001800-34010800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr17:34001800-34014000	Weak transcription	Right Ventricle	heart
20	chr17:34001800-34014800	Weak transcription	Brain Substantia Nigra	brain
21	chr17:34001800-34018200	Weak transcription	Esophagus	oesophagus
22	chr17:34002000-34010600	Weak transcription	HSMMtube	muscle
23	chr17:34002000-34017400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:34002000-34032200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:34002000-34036800	Weak transcription	Colonic Mucosa	Colon
26	chr17:34002200-34011600	Weak transcription	HepG2	liver
27	chr17:34002200-34014600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:34002200-34015000	Weak transcription	HUVEC	blood vessel
29	chr17:34002200-34017000	Weak transcription	Brain Angular Gyrus	brain
30	chr17:34002400-34013200	Weak transcription	Brain Germinal Matrix	brain
31	chr17:34003800-34010600	Weak transcription	Primary B cells from cord blood	blood
32	chr17:34004600-34011800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:34004800-34016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:34005400-34011400	Strong transcription	Fetal Lung	lung
35	chr17:34005400-34024400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr17:34005400-34028400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:34005600-34011800	Strong transcription	Adipose Nuclei	Adipose
38	chr17:34005600-34018800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:34005600-34024400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr17:34005800-34012000	Strong transcription	Primary T cells from cord blood	blood
41	chr17:34005800-34026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:34006000-34024400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:34006200-34010600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr17:34006200-34011000	Strong transcription	Fetal Stomach	stomach
45	chr17:34006200-34011200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr17:34006200-34018800	Strong transcription	Fetal Muscle Leg	muscle
47	chr17:34006200-34018800	Strong transcription	Dnd41	blood
48	chr17:34006400-34012000	Strong transcription	Liver	Liver
49	chr17:34006400-34018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:34006400-34019000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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