Variant report

Variant	rs10854010
Chromosome Location	chr19:19290437-19290438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19239263..19241011-chr19:19289678..19291212,2	K562	blood:
2	chr19:19286456..19293705-chr19:19298673..19304955,13	K562	blood:
3	chr19:19288334..19290491-chr19:19291596..19294334,2	K562	blood:
4	chr19:19289152..19291320-chr19:19372461..19375082,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000064490	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000187664	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10854011	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085254	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11668300	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668319	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671619	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878301	0.80[EUR][1000 genomes]
rs12162246	0.80[EUR][1000 genomes]
rs12162274	0.80[EUR][1000 genomes]
rs12974661	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2157850	0.80[EUR][1000 genomes]
rs2283618	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283619	0.90[ASN][1000 genomes]
rs2283622	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34719098	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3819578	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890384	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4471820	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57157462	0.80[EUR][1000 genomes]
rs59829545	0.80[EUR][1000 genomes]
rs59953916	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60636572	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61061000	0.85[AFR][1000 genomes]
rs66764858	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66907536	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67238925	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67239864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67801643	0.80[EUR][1000 genomes]
rs67845377	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72997105	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73535580	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73537429	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537449	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10854010	MEF2B	cis	Thyroid	GTEx
rs10854010	MEF2B	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
2	chr19:19280800-19301600	Weak transcription	NHEK	skin
3	chr19:19281400-19292200	Weak transcription	HMEC	breast
4	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:19281600-19290600	Weak transcription	Fetal Brain Female	brain
6	chr19:19281600-19290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:19281600-19290800	Weak transcription	Brain Angular Gyrus	brain
8	chr19:19281600-19292000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:19281600-19302000	Weak transcription	NH-A	brain
14	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:19281800-19290600	Weak transcription	Brain Germinal Matrix	brain
16	chr19:19281800-19300000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:19281800-19301200	Weak transcription	Stomach Mucosa	stomach
18	chr19:19282000-19292200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:19282000-19301600	Weak transcription	Fetal Heart	heart
20	chr19:19283000-19292200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:19283400-19290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:19283400-19290800	Weak transcription	A549	lung
23	chr19:19283400-19291000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:19283400-19292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:19283400-19300600	Weak transcription	Psoas Muscle	Psoas
26	chr19:19283400-19301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:19283400-19302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:19283400-19302200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:19283600-19301800	Weak transcription	HSMMtube	muscle
30	chr19:19283800-19291000	Weak transcription	Hela-S3	cervix
31	chr19:19283800-19292200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:19284200-19302000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:19284600-19290800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:19285400-19290800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:19285600-19301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:19286000-19290600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:19286000-19290600	Weak transcription	GM12878-XiMat	blood
38	chr19:19286000-19290800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:19286000-19290800	Strong transcription	Fetal Stomach	stomach
40	chr19:19286000-19292800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:19286000-19301000	Weak transcription	HepG2	liver
42	chr19:19286000-19302000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:19286400-19290600	Strong transcription	Fetal Intestine Small	intestine
44	chr19:19286400-19290800	Strong transcription	Spleen	Spleen
45	chr19:19286400-19294000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:19286600-19290800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:19286600-19290800	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:19286600-19293600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr19:19286600-19293600	Strong transcription	Ovary	ovary
50	chr19:19286600-19293800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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