Variant report

Variant	rs3890434
Chromosome Location	chr19:51832271-51832272
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51831663..51834419-chr19:51869763..51871629,2	MCF-7	breast:
2	chr19:51821473..51823023-chr19:51829659..51832383,2	K562	blood:
3	chr19:51826171..51828199-chr19:51829829..51832317,2	K562	blood:
4	chr19:51829374..51832603-chr19:51869353..51873861,5	K562	blood:
5	chr19:51829638..51832503-chr19:52050785..52052514,2	K562	blood:
6	chr19:51829665..51832508-chr19:51897331..51898957,2	K562	blood:
7	chr19:51821207..51828199-chr19:51828688..51832317,8	K562	blood:
8	chr19:51828803..51835205-chr19:51840657..51845313,13	K562	blood:
9	chr19:51828870..51832603-chr19:51869722..51873861,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160318	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000105379	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10414554	1.00[JPT][hapmap]
rs10424572	1.00[JPT][hapmap]
rs10425109	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3890434	SERPINA1	trans	lymphoblastoid	seeQTL
rs3890434	PPP4R4	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51827400-51833800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:51829600-51833600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:51831000-51832400	Weak transcription	Brain Germinal Matrix	brain
4	chr19:51831000-51834600	Weak transcription	Gastric	stomach
5	chr19:51831000-51837000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:51831000-51841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:51831200-51832800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:51831200-51833200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:51831200-51834400	Weak transcription	Pancreas	Pancrea
10	chr19:51831200-51834600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:51831400-51833600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:51831400-51833800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:51831400-51834600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:51831400-51835000	Weak transcription	HepG2	liver
15	chr19:51831400-51841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:51831600-51832400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr19:51831600-51832600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:51831600-51833000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:51831600-51833600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:51831600-51833800	Weak transcription	A549	lung
21	chr19:51831600-51834400	Weak transcription	Liver	Liver
22	chr19:51831600-51834600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:51831600-51835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:51831600-51841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:51832000-51833600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:51832000-51834200	Strong transcription	Fetal Brain Female	brain
27	chr19:51832200-51832400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:51832200-51834000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:51832200-51841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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