Variant report

Variant	rs888994
Chromosome Location	chr19:39115552-39115553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39114786-39115761	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:39115284-39115786	K562	blood:	n/a	n/a
3	POLR2A	chr19:39114094-39125094	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39115347-39115691	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:39114766-39115867	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:39115378-39115982	K562	blood:	n/a	n/a
7	POLR2A	chr19:39114328-39115801	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr19:39114179-39115838	K562	blood:	n/a	n/a
9	POLR2A	chr19:39114198-39115775	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:39113935-39116258	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:39115333-39115786	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39110019..39112563-chr19:39114565..39116465,2	MCF-7	breast:
2	chr19:39108860..39110529-chr19:39114006..39115953,2	MCF-7	breast:
3	chr19:39113439..39116132-chr19:39174637..39176541,2	MCF-7	breast:

Variant related genes	Relation type
EIF3K	TF binding region
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10445564	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12976749	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.96[ASN][1000 genomes]
rs12977469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13345885	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs1862371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1978443	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2232992	0.87[CEU][hapmap];0.96[TSI][hapmap]
rs2287732	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs2287733	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs3786834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4592774	0.86[EUR][1000 genomes]
rs62120354	0.84[EUR][1000 genomes]
rs62120358	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7251456	0.81[CEU][hapmap]
rs750438	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9304576	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs888994	PLAUR	cis	cerebellum	SCAN
rs888994	GSK3A	cis	cerebellum	SCAN
rs888994	LYPD4	cis	parietal	SCAN
rs888994	AP2S1	cis	cerebellum	SCAN
rs888994	ZFP36	cis	parietal	SCAN
rs888994	SELV	cis	parietal	SCAN
rs888994	TMEM145	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39110400-39122600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39110800-39118000	Weak transcription	Fetal Kidney	kidney
3	chr19:39110800-39120800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr19:39110800-39120800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:39111000-39121000	Strong transcription	Ovary	ovary
6	chr19:39111000-39121600	Strong transcription	Fetal Intestine Large	intestine
7	chr19:39111000-39122600	Strong transcription	Fetal Intestine Small	intestine
8	chr19:39111000-39124000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:39111000-39124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:39111000-39124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:39111000-39125000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
13	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:39111200-39116400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:39111200-39118200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr19:39111200-39120600	Strong transcription	HMEC	breast
18	chr19:39111200-39120800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:39111200-39120800	Strong transcription	Gastric	stomach
20	chr19:39111200-39120800	Strong transcription	HUVEC	blood vessel
21	chr19:39111200-39121000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:39111200-39121400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:39111200-39121400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:39111200-39121600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:39111200-39121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:39111200-39121600	Strong transcription	Right Ventricle	heart
27	chr19:39111200-39121800	Strong transcription	Brain Cingulate Gyrus	brain
28	chr19:39111200-39121800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:39111200-39122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:39111200-39122400	Strong transcription	Colonic Mucosa	Colon
31	chr19:39111200-39123600	Strong transcription	Osteobl	bone
32	chr19:39111200-39123800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr19:39111200-39123800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:39111200-39123800	Strong transcription	Primary T cells from cord blood	blood
35	chr19:39111200-39124000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:39111200-39124000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:39111200-39124000	Strong transcription	Liver	Liver
38	chr19:39111200-39124000	Strong transcription	Brain Angular Gyrus	brain
39	chr19:39111200-39124000	Strong transcription	Placenta	Placenta
40	chr19:39111200-39124000	Strong transcription	Fetal Thymus	thymus
41	chr19:39111200-39124000	Strong transcription	Left Ventricle	heart
42	chr19:39111200-39124000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr19:39111200-39124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:39111200-39124200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:39111200-39124200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:39111200-39124200	Strong transcription	Brain Germinal Matrix	brain
47	chr19:39111200-39124200	Strong transcription	Fetal Brain Female	brain
48	chr19:39111200-39124200	Strong transcription	Lung	lung
49	chr19:39111200-39124400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:39111200-39124400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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