Variant report

Variant	rs890934
Chromosome Location	chr19:41227968-41227969
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41227762-41228664	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:41227937-41228620	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr19:41227922-41228303	MCF10A-Er-Src	breast:	n/a	n/a
6	NR3C1	chr19:41227880-41228605	A549	lung:	n/a	n/a
7	NR3C1	chr19:41227944-41228586	A549	lung:	n/a	n/a
8	POLR2A	chr19:41227926-41228524	HUVEC	blood vessel:	n/a	n/a
9	FOS	chr19:41227965-41228635	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41219786..41224599-chr19:41225550..41230033,6	K562	blood:
2	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
3	chr19:41227271..41230078-chr19:41282801..41284516,2	MCF-7	breast:
4	chr19:41220671..41224766-chr19:41226443..41229963,4	K562	blood:
5	chr19:41224979..41226592-chr19:41227722..41229766,2	K562	blood:
6	chr19:41168010..41170261-chr19:41227028..41229783,2	MCF-7	breast:
7	chr19:41226837..41229438-chr19:41260513..41263205,2	MCF-7	breast:
8	chr19:41225019..41226612-chr19:41226846..41228411,3	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10425765	0.87[AFR][1000 genomes]
rs11083566	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap]
rs1469427	0.82[AFR][1000 genomes]
rs1870087	0.93[YRI][hapmap]
rs2290692	0.93[YRI][hapmap]
rs2561547	0.81[JPT][hapmap]
rs7248570	0.87[ASW][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs7251246	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs7257602	0.81[ASW][hapmap];0.82[LWK][hapmap];0.80[AFR][1000 genomes]
rs7260405	0.83[AFR][1000 genomes]

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	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	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
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs890934	KCNN4	cis	cerebellum	SCAN
rs890934	SULT2B1	cis	cerebellum	SCAN
rs890934	APOC4	cis	cerebellum	SCAN
rs890934	RAB4B,MIA	cis	brain	BrainEAC
rs890934	EHD2	cis	cerebellum	SCAN
rs890934	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41224800-41228600	Enhancers	Fetal Brain Male	brain
2	chr19:41225000-41228400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:41225200-41228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:41225200-41229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:41225200-41229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:41225600-41229800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:41225800-41228000	Weak transcription	A549	lung
13	chr19:41225800-41228200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr19:41225800-41228400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:41225800-41229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:41225800-41229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:41225800-41229800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:41225800-41229800	Weak transcription	Thymus	Thymus
19	chr19:41225800-41232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:41225800-41232200	Weak transcription	Fetal Kidney	kidney
21	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:41226400-41228400	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr19:41226400-41228600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:41226400-41228600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:41226400-41228600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:41226400-41228600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:41226400-41228800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr19:41226400-41229600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:41226600-41228200	Enhancers	HepG2	liver
33	chr19:41226600-41228800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:41226600-41229200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:41226800-41228000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:41226800-41228000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:41226800-41228000	Weak transcription	Hela-S3	cervix
40	chr19:41226800-41228000	Weak transcription	NH-A	brain
41	chr19:41226800-41228200	Weak transcription	Primary B cells from cord blood	blood
42	chr19:41226800-41228400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:41226800-41228600	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr19:41226800-41228600	Enhancers	Small Intestine	intestine
45	chr19:41226800-41228800	Genic enhancers	Placenta Amnion	Placenta Amnion
46	chr19:41226800-41229800	Weak transcription	Primary T cells from cord blood	blood
47	chr19:41226800-41230000	Weak transcription	HSMMtube	muscle
48	chr19:41226800-41236600	Weak transcription	GM12878-XiMat	blood
49	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links