Variant report

Variant	rs12460049
Chromosome Location	chr19:37150349-37150350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF461-4	chr19:37150031-37150379	l_1676_chr19:37148392-37193298_testes

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10408063	1.00[ASN][1000 genomes]
rs10410939	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10411150	0.90[ASN][1000 genomes]
rs10413876	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10414240	1.00[ASN][1000 genomes]
rs10418271	1.00[ASN][1000 genomes]
rs11880022	1.00[ASN][1000 genomes]
rs11880159	1.00[ASN][1000 genomes]
rs1227559	1.00[ASN][1000 genomes]
rs1227561	1.00[ASN][1000 genomes]
rs12459208	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12459218	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12459243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459325	1.00[ASN][1000 genomes]
rs12459377	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12459429	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459527	1.00[ASN][1000 genomes]
rs12459808	1.00[ASN][1000 genomes]
rs12459894	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12459915	1.00[ASN][1000 genomes]
rs12459923	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460354	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460418	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460420	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12460430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460455	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460482	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12460774	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461023	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461264	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461265	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461280	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12461954	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12461970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462037	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462268	1.00[ASN][1000 genomes]
rs12462281	1.00[ASN][1000 genomes]
rs12462325	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462454	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12462471	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12462635	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12462921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12463012	0.90[ASN][1000 genomes]
rs12974130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1625762	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1643422	1.00[CHB][hapmap]
rs1673083	1.00[ASN][1000 genomes]
rs16971568	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[ASN][1000 genomes]
rs16973489	1.00[ASN][1000 genomes]
rs17468285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs1990964	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs25419	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[ASN][1000 genomes]
rs28398875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28465595	1.00[ASN][1000 genomes]
rs28472526	1.00[ASN][1000 genomes]
rs28645577	1.00[ASN][1000 genomes]
rs28742010	1.00[ASN][1000 genomes]
rs28818888	1.00[ASN][1000 genomes]
rs34051375	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34106502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35621405	1.00[ASN][1000 genomes]
rs35706444	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3859520	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs491951	0.90[ASN][1000 genomes]
rs500244	0.90[ASN][1000 genomes]
rs58245911	1.00[ASN][1000 genomes]
rs60268308	1.00[ASN][1000 genomes]
rs60615280	1.00[ASN][1000 genomes]
rs61750934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6510562	1.00[ASN][1000 genomes]
rs73609133	1.00[ASN][1000 genomes]
rs73612031	1.00[ASN][1000 genomes]
rs73612043	1.00[ASN][1000 genomes]
rs73615692	1.00[ASN][1000 genomes]
rs73615693	0.90[ASN][1000 genomes]
rs7508258	1.00[ASN][1000 genomes]
rs8104355	0.90[ASN][1000 genomes]
rs8107274	1.00[CHB][hapmap]
rs8111419	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
10	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv1061250	chr19:37134068-37188771	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
14	esv34384	chr19:37134068-37330613	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	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
4	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:37110400-37152600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:37124800-37155600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37126200-37156200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:37127200-37151000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:37128200-37150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:37128800-37156200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:37134600-37157000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:37135200-37156200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:37135800-37150800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:37135800-37156200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr19:37135800-37156400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:37136000-37150800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:37136000-37151600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:37136000-37152200	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:37136000-37152400	ZNF genes & repeats	A549	lung
20	chr19:37136400-37152200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr19:37137200-37150400	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr19:37137200-37151200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr19:37141400-37150800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr19:37141400-37151000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr19:37141400-37151000	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:37141400-37151200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:37141800-37150600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:37141800-37150800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:37142600-37156000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr19:37143400-37154600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:37143600-37150400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr19:37143600-37151000	Strong transcription	Placenta	Placenta
33	chr19:37143600-37152200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
34	chr19:37143600-37156800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:37144200-37152200	ZNF genes & repeats	Small Intestine	intestine
36	chr19:37144400-37156000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:37144600-37150800	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr19:37145200-37156600	Weak transcription	Fetal Heart	heart
39	chr19:37145400-37150600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:37145600-37153400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:37145600-37156600	Weak transcription	NHLF	lung
42	chr19:37145600-37156800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:37146600-37151000	Strong transcription	Brain Anterior Caudate	brain
44	chr19:37147400-37151000	Strong transcription	Dnd41	blood
45	chr19:37147400-37154200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:37147400-37156600	Weak transcription	NHEK	skin
47	chr19:37147600-37152000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:37147600-37156600	Weak transcription	HMEC	breast
49	chr19:37147800-37151200	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:37148000-37151200	Strong transcription	Primary T cells fromperipheralblood	blood

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