Variant report

Variant	rs248933
Chromosome Location	chr19:19899564-19899565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-3	chr19:19899564-19899938	ENSG00000267481.1

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10404296	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412885	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12710110	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs16996360	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248930	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248931	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248932	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248934	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248936	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248937	0.81[EUR][1000 genomes]
rs248942	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248948	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248949	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248951	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248952	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248954	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762190	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808989	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4808991	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808995	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246727	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256535	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106100	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109240	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111421	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs248933	ZNF93	cis	cerebellum	SCAN
rs248933	ATP13A1	cis	parietal	SCAN
rs248933	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs248933	ZNF506	cis	normal skin	skin_eQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888000-19899600	Weak transcription	Ovary	ovary
2	chr19:19888200-19902200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
4	chr19:19888600-19899600	Weak transcription	Brain Germinal Matrix	brain
5	chr19:19888600-19899600	Weak transcription	Colonic Mucosa	Colon
6	chr19:19888600-19901000	Weak transcription	HMEC	breast
7	chr19:19888600-19901800	Weak transcription	Small Intestine	intestine
8	chr19:19888600-19902000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:19888600-19904000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:19888600-19906400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:19888600-19906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:19888600-19909000	Weak transcription	K562	blood
13	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
14	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
15	chr19:19888800-19899600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:19888800-19900400	Weak transcription	Stomach Mucosa	stomach
17	chr19:19888800-19900800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:19888800-19904000	Weak transcription	Hela-S3	cervix
19	chr19:19889600-19899600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:19889600-19902000	Weak transcription	NHDF-Ad	bronchial
21	chr19:19889600-19904600	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:19890400-19902600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:19890600-19899600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:19892000-19899600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:19892200-19899600	Weak transcription	Fetal Kidney	kidney
26	chr19:19894000-19899600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:19894200-19904400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:19895400-19908200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:19895600-19902800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:19895600-19903000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:19895600-19903200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:19895600-19903400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:19895600-19904200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:19895600-19907200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:19895600-19909000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr19:19895600-19909000	ZNF genes & repeats	Liver	Liver
40	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr19:19895800-19900200	ZNF genes & repeats	GM12878-XiMat	blood
43	chr19:19895800-19901800	Strong transcription	Fetal Stomach	stomach
44	chr19:19895800-19903000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr19:19895800-19903400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:19895800-19908200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:19895800-19914800	Strong transcription	Dnd41	blood
48	chr19:19896000-19903600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:19896000-19909200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:19896200-19903000	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links