Variant report

Variant	rs539
Chromosome Location	chr19:19287802-19287803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19286456..19293705-chr19:19298673..19304955,13	K562	blood:
2	chr19:19285194..19288859-chr19:19295274..19298317,3	K562	blood:
3	chr19:19280512..19282553-chr19:19286419..19290416,4	K562	blood:
4	chr19:19287450..19289684-chr19:19301395..19303097,2	MCF-7	breast:
5	chr19:19284383..19288612-chr19:19288854..19291941,5	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM161A-1	chr19:19287714-19288269	NONHSAT063026
2	lnc-TMEM161A-1	chr19:19287713-19291410	NONHSAT063025

No data

Variant related genes	Relation type
ENSG00000064489	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064490	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1005980	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10417796	0.85[EUR][1000 genomes]
rs10418053	0.96[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs1050544	0.96[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10854008	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854009	0.84[EUR][1000 genomes]
rs10854012	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11669408	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669860	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669861	0.87[EUR][1000 genomes]
rs12609573	1.00[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12972894	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974672	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975253	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975290	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980269	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12980955	0.84[EUR][1000 genomes]
rs12981160	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858846	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239369	0.94[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2239370	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2283623	0.84[EUR][1000 genomes]
rs2314035	0.85[EUR][1000 genomes]
rs35342977	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3787040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808185	0.83[EUR][1000 genomes]
rs62135499	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71332145	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7260127	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72997174	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs741706	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8101388	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs539	ZNF682	cis	parietal	SCAN
rs539	RAB8A	cis	parietal	SCAN
rs539	PDE4C	cis	cerebellum	SCAN
rs539	C19orf50	cis	cerebellum	SCAN
rs539	C19orf50	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
2	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
3	chr19:19280800-19301600	Weak transcription	NHEK	skin
4	chr19:19281400-19290200	Weak transcription	Brain Substantia Nigra	brain
5	chr19:19281400-19292200	Weak transcription	HMEC	breast
6	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:19281600-19289000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:19281600-19290400	Weak transcription	Fetal Lung	lung
9	chr19:19281600-19290600	Weak transcription	Fetal Brain Female	brain
10	chr19:19281600-19290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:19281600-19290800	Weak transcription	Brain Angular Gyrus	brain
12	chr19:19281600-19292000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:19281600-19302000	Weak transcription	NH-A	brain
18	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:19281800-19289200	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:19281800-19290600	Weak transcription	Brain Germinal Matrix	brain
21	chr19:19281800-19300000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:19281800-19301200	Weak transcription	Stomach Mucosa	stomach
23	chr19:19282000-19292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:19282000-19301600	Weak transcription	Fetal Heart	heart
25	chr19:19283000-19292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:19283400-19290200	Weak transcription	NHLF	lung
27	chr19:19283400-19290400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:19283400-19290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:19283400-19290800	Weak transcription	A549	lung
30	chr19:19283400-19291000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:19283400-19292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:19283400-19300600	Weak transcription	Psoas Muscle	Psoas
33	chr19:19283400-19301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:19283400-19302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:19283400-19302200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:19283600-19301800	Weak transcription	HSMMtube	muscle
37	chr19:19283800-19290200	Weak transcription	Osteobl	bone
38	chr19:19283800-19291000	Weak transcription	Hela-S3	cervix
39	chr19:19283800-19292200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:19284200-19302000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:19284600-19290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:19285400-19290800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:19285600-19301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:19286000-19290200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:19286000-19290400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:19286000-19290600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:19286000-19290600	Weak transcription	GM12878-XiMat	blood
48	chr19:19286000-19290800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:19286000-19290800	Strong transcription	Fetal Stomach	stomach
50	chr19:19286000-19292800	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links