Variant report

Variant	rs2561549
Chromosome Location	chr19:41174483-41174484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
2	chr19:41167833..41170600-chr19:41173317..41176394,3	MCF-7	breast:
3	chr19:41167372..41175149-chr19:41187518..41198541,22	K562	blood:
4	chr19:41171985..41176323-chr19:41183438..41185742,3	MCF-7	breast:
5	chr19:41173473..41175740-chr19:41257200..41259072,2	MCF-7	breast:
6	chr19:41173668..41175905-chr19:41178921..41181635,2	K562	blood:
7	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:

Variant related genes	Relation type
ENSG00000077312	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000188493	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2250994	0.99[ASN][1000 genomes]
rs2561539	0.92[ASN][1000 genomes]
rs2561542	0.92[ASN][1000 genomes]
rs2561543	0.93[ASN][1000 genomes]
rs2561546	0.94[ASN][1000 genomes]
rs2561548	0.99[ASN][1000 genomes]
rs2604892	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2604900	0.99[ASN][1000 genomes]
rs8110611	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2561549	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41169800-41175000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:41169800-41175000	Weak transcription	Brain Substantia Nigra	brain
3	chr19:41169800-41175000	Weak transcription	Fetal Heart	heart
4	chr19:41169800-41175000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:41169800-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
7	chr19:41170000-41174600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:41170000-41174600	Weak transcription	Primary B cells from cord blood	blood
9	chr19:41170000-41174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:41170000-41174600	Weak transcription	Fetal Thymus	thymus
11	chr19:41170000-41174800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:41170000-41175000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:41170000-41175000	Weak transcription	GM12878-XiMat	blood
14	chr19:41170000-41175200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:41170000-41175400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:41170000-41178400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:41170000-41180400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:41170000-41180400	Weak transcription	Right Atrium	heart
19	chr19:41170000-41180800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:41170200-41174600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr19:41170200-41174600	Weak transcription	Fetal Brain Male	brain
22	chr19:41170200-41174600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:41170200-41174800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr19:41170200-41174800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:41170200-41175000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:41172000-41193000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:41172200-41175000	Strong transcription	Brain Germinal Matrix	brain
28	chr19:41172200-41175600	Strong transcription	Fetal Stomach	stomach
29	chr19:41172400-41174600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr19:41172400-41174800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:41172400-41174800	Strong transcription	Fetal Brain Female	brain
32	chr19:41172400-41191000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:41172600-41174800	Strong transcription	Fetal Intestine Small	intestine
34	chr19:41172600-41174800	Strong transcription	Fetal Muscle Leg	muscle
35	chr19:41172600-41175400	Strong transcription	Lung	lung
36	chr19:41172600-41176200	Strong transcription	NHLF	lung
37	chr19:41172600-41193400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:41172600-41193600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr19:41172800-41174800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:41172800-41174800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:41172800-41175000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:41172800-41175200	Strong transcription	Spleen	Spleen
43	chr19:41172800-41175400	Strong transcription	Brain Hippocampus Middle	brain
44	chr19:41172800-41180000	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:41172800-41180200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:41172800-41180600	Strong transcription	Liver	Liver
47	chr19:41172800-41180800	Strong transcription	Colonic Mucosa	Colon
48	chr19:41172800-41191000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:41172800-41192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:41172800-41192800	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links