Variant report

Variant	rs1654624
Chromosome Location	chr19:42868217-42868218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42863507..42865168-chr19:42867333..42869405,2	K562	blood:
2	chr19:42859791..42861362-chr19:42867792..42869534,2	K562	blood:
3	chr19:42866425..42869434-chr19:42871814..42873875,3	K562	blood:
4	chr19:42856129..42858540-chr19:42867556..42869404,2	MCF-7	breast:
5	chr19:42862702..42865625-chr19:42867333..42870442,3	K562	blood:

Variant related genes	Relation type
ENSG00000105429	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1206029	0.82[ASW][hapmap];0.87[YRI][hapmap]
rs1206030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1206033	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs1206036	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1206037	1.00[AMR][1000 genomes]
rs1206039	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1685564	0.82[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1685565	1.00[YRI][hapmap]
rs1685566	0.87[AFR][1000 genomes]
rs2615615	1.00[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs851291	1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs851295	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs851299	1.00[AMR][1000 genomes]
rs851300	1.00[AMR][1000 genomes]
rs851608	1.00[AMR][1000 genomes]
rs851611	0.83[AFR][1000 genomes]
rs851614	1.00[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1654624	TMEM145	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
2	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr19:42831000-42874400	Weak transcription	HSMM	muscle
4	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:42831800-42873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:42831800-42874800	Weak transcription	K562	blood
7	chr19:42844800-42877400	Weak transcription	Stomach Mucosa	stomach
8	chr19:42852000-42868600	Strong transcription	Fetal Muscle Leg	muscle
9	chr19:42856400-42869000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr19:42857400-42869600	Strong transcription	Brain Germinal Matrix	brain
11	chr19:42857600-42870800	Strong transcription	Fetal Brain Female	brain
12	chr19:42857800-42868800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:42857800-42871000	Weak transcription	Fetal Brain Male	brain
14	chr19:42857800-42874000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:42858200-42872200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:42861800-42869000	Weak transcription	Psoas Muscle	Psoas
17	chr19:42862400-42873800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:42862600-42878800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:42863600-42874800	Weak transcription	HUVEC	blood vessel
20	chr19:42864600-42868600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:42864600-42868600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr19:42864800-42868800	Strong transcription	Fetal Lung	lung
23	chr19:42865000-42869000	Strong transcription	Brain Hippocampus Middle	brain
24	chr19:42865000-42869200	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr19:42865200-42869000	Strong transcription	Brain Angular Gyrus	brain
26	chr19:42865200-42869000	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:42865200-42869200	Strong transcription	Brain Anterior Caudate	brain
28	chr19:42865200-42869600	Strong transcription	Pancreas	Pancrea
29	chr19:42865200-42873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:42865400-42868800	Strong transcription	Dnd41	blood
31	chr19:42865800-42869000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:42866000-42868400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:42866000-42869200	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr19:42866200-42868800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:42866400-42868400	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr19:42866400-42869000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:42866600-42868800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:42866600-42871600	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:42866800-42868400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr19:42866800-42869000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:42866800-42869800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:42867000-42868400	ZNF genes & repeats	Ovary	ovary
43	chr19:42867200-42868400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr19:42867200-42868400	Strong transcription	HSMMtube	muscle
45	chr19:42867200-42868600	ZNF genes & repeats	Aorta	Aorta
46	chr19:42867200-42868800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
47	chr19:42867200-42868800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:42867200-42868800	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr19:42867200-42869400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:42867200-42871000	Enhancers	Primary B cells from cord blood	blood

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