Variant report

Variant	rs454904
Chromosome Location	chr19:44511589-44511590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44438985..44440520-chr19:44510451..44513064,2	MCF-7	breast:
2	chr19:44506929..44508722-chr19:44508906..44512991,6	K562	blood:
3	chr19:44510545..44512229-chr19:44575902..44577637,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124459	Chromatin interaction
ENSG00000266921	Chromatin interaction
ENSG00000186026	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1107064	0.82[ASW][hapmap]
rs11083734	0.86[ASN][1000 genomes]
rs11083735	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083736	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083737	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11666432	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12610472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1474061	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1996409	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138823	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2138824	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2176431	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2284243	1.00[YRI][hapmap]
rs2356537	1.00[YRI][hapmap]
rs382197	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3826941	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4239528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs427608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4299256	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4371266	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4375771	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4444434	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs451388	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4550576	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4555257	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803668	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803672	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803674	0.91[CHB][hapmap];0.89[GIH][hapmap]
rs55798868	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56003307	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56230322	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56250154	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57895932	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62119177	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6509135	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6509137	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7251015	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252213	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7255192	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7257809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8105003	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109313	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8109615	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110348	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9646633	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs454904	C14orf50	trans	parietal	SCAN
rs454904	ZNF223	cis	Nerve Tibial	GTEx
rs454904	FUT2	cis	parietal	SCAN
rs454904	ZNF284	cis	lymphoblastoid	seeQTL
rs454904	ZNF223	cis	Thyroid	GTEx
rs454904	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs454904	ZNF223	cis	Esophagus Mucosa	GTEx
rs454904	ETFB	cis	parietal	SCAN
rs454904	OPA3	cis	parietal	SCAN
rs454904	ASPDH	cis	cerebellum	SCAN
rs454904	SPHK2	cis	parietal	SCAN
rs454904	ZNF613	cis	parietal	SCAN
rs454904	HIF3A	cis	parietal	SCAN
rs454904	EMP3	cis	parietal	SCAN
rs454904	KPTN	cis	parietal	SCAN
rs454904	APOC2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44508000-44511600	Weak transcription	Pancreas	Pancrea
2	chr19:44508200-44511600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:44508200-44511600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44508200-44511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:44508200-44511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:44508200-44511800	Weak transcription	Stomach Mucosa	stomach
7	chr19:44508200-44512000	Weak transcription	HSMM	muscle
8	chr19:44508200-44512800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:44508400-44511600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:44508400-44511600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:44508400-44511600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:44508400-44511600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:44508400-44511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:44508400-44511600	Weak transcription	Fetal Stomach	stomach
15	chr19:44508400-44511600	Weak transcription	HepG2	liver
16	chr19:44508400-44511600	Weak transcription	NHEK	skin
17	chr19:44508400-44511600	Weak transcription	NHLF	lung
18	chr19:44508400-44511800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:44508400-44512000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:44508400-44512000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:44508400-44512000	Weak transcription	HSMMtube	muscle
22	chr19:44508400-44512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:44508400-44512200	Weak transcription	HMEC	breast
24	chr19:44508400-44512800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:44508400-44513000	Weak transcription	K562	blood
26	chr19:44508400-44513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:44508400-44513600	Weak transcription	Hela-S3	cervix
28	chr19:44508600-44512600	Weak transcription	NHDF-Ad	bronchial
29	chr19:44509200-44520600	ZNF genes & repeats	Liver	Liver
30	chr19:44509400-44516800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:44509400-44518200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:44509800-44516600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
33	chr19:44509800-44517000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:44509800-44517400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr19:44510000-44517000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr19:44510000-44517000	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr19:44510000-44517200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
38	chr19:44510000-44517400	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:44510200-44512000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:44510200-44513000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:44510200-44516600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
42	chr19:44510200-44517000	ZNF genes & repeats	GM12878-XiMat	blood
43	chr19:44510200-44517400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
44	chr19:44510200-44517600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr19:44510400-44516400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:44510400-44517200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
47	chr19:44510400-44517600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:44510400-44517600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
49	chr19:44510600-44513200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:44510600-44513600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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