Variant report

Variant	rs3791642
Chromosome Location	chr2:55572944-55572945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS27A-1	chr2:55572493-55573185	ENSG00000240401.4

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10169395	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10172058	0.84[ASN][1000 genomes]
rs10194425	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496042	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11125564	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11125573	0.90[CHB][hapmap]
rs11678347	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614357	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617887	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621495	0.83[CHB][hapmap]
rs12623605	0.91[CHB][hapmap]
rs12713293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12713294	0.88[ASN][1000 genomes]
rs12713295	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12713296	0.86[CHB][hapmap]
rs13001912	0.88[ASN][1000 genomes]
rs13010237	0.81[ASN][1000 genomes]
rs13013113	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13019339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022424	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13028925	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389156	0.91[CHB][hapmap]
rs1344881	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs1349884	0.88[ASN][1000 genomes]
rs1349885	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1370360	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370361	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1902060	0.91[CHB][hapmap]
rs2198575	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2576687	0.82[AFR][1000 genomes]
rs2576704	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs2576716	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs2576717	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs2589065	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs2589077	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs2589090	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs2589103	0.87[AFR][1000 genomes]
rs2867174	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2867175	0.86[ASN][1000 genomes]
rs2867176	0.86[ASN][1000 genomes]
rs2867177	0.86[ASN][1000 genomes]
rs2920964	0.91[AFR][1000 genomes]
rs2920974	0.85[YRI][hapmap]
rs2966467	0.91[AFR][1000 genomes]
rs3791650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828235	0.91[CHB][hapmap]
rs66882175	0.90[ASN][1000 genomes]
rs6724338	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6746104	0.91[CHB][hapmap]
rs6747649	0.91[CHB][hapmap]
rs6752182	0.89[ASN][1000 genomes]
rs6754930	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756777	0.86[ASN][1000 genomes]
rs74181227	0.89[ASN][1000 genomes]
rs7558687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7561473	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7569535	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7576695	0.88[AFR][1000 genomes]
rs7589390	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7600339	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
4	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
6	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
9	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
12	chr2:55537800-55609400	Weak transcription	Lung	lung
13	chr2:55539200-55579000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55539200-55579000	Weak transcription	NHEK	skin
15	chr2:55541400-55584400	Weak transcription	Spleen	Spleen
16	chr2:55541800-55574800	Weak transcription	Ovary	ovary
17	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
19	chr2:55544200-55581800	Weak transcription	Left Ventricle	heart
20	chr2:55546200-55585000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:55546600-55579000	Weak transcription	K562	blood
22	chr2:55546800-55578800	Weak transcription	GM12878-XiMat	blood
23	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:55548200-55585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:55548600-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:55548800-55574800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:55551800-55577000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:55553400-55577200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:55554600-55577200	Weak transcription	Placenta	Placenta
30	chr2:55554800-55584200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
32	chr2:55555000-55582200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:55555200-55574400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:55555200-55578800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:55555800-55586000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:55556600-55579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:55557000-55578600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:55558000-55578600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
41	chr2:55559200-55578800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:55560400-55578800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:55560600-55575000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:55560600-55578800	Weak transcription	Fetal Brain Male	brain
45	chr2:55560800-55573000	Weak transcription	HMEC	breast
46	chr2:55563600-55574800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:55563600-55578800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:55563600-55579200	Weak transcription	Thymus	Thymus
49	chr2:55563600-55584400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney

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