Variant report

Variant	rs16983548
Chromosome Location	chr19:52701052-52701053
allele	C/G
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	chr19:52700633-52702232	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:52700566-52701984	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:52700939-52701613	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:52700471-52701062	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:52700374-52702369	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52689327..52690920-chr19:52699885..52701616,2	MCF-7	breast:
2	chr19:52700388..52702359-chr19:52712613..52714354,3	K562	blood:

Variant related genes	Relation type
PPP2R1A	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1025279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402209	1.00[JPT][hapmap]
rs10403154	1.00[JPT][hapmap]
rs10403202	1.00[JPT][hapmap]
rs10403806	1.00[JPT][hapmap]
rs10404236	1.00[JPT][hapmap]
rs10405293	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10405856	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10405862	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10407502	1.00[JPT][hapmap]
rs10407987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408119	1.00[JPT][hapmap]
rs10410908	0.88[CEU][hapmap]
rs10411335	0.88[CEU][hapmap]
rs10413274	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10413435	1.00[JPT][hapmap]
rs10413470	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10413847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10414083	1.00[JPT][hapmap]
rs10414197	1.00[JPT][hapmap]
rs10414423	1.00[JPT][hapmap]
rs10414852	1.00[JPT][hapmap]
rs10416195	0.84[EUR][1000 genomes]
rs10417253	1.00[JPT][hapmap]
rs10417820	1.00[JPT][hapmap]
rs10419304	1.00[JPT][hapmap]
rs10420254	1.00[JPT][hapmap]
rs10422483	1.00[JPT][hapmap]
rs10422583	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422838	1.00[JPT][hapmap]
rs10423610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425135	1.00[JPT][hapmap]
rs10425393	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426066	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426786	1.00[JPT][hapmap]
rs1056348	1.00[JPT][hapmap]
rs11879419	1.00[JPT][hapmap]
rs13344984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16983549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983598	1.00[JPT][hapmap]
rs16983603	1.00[JPT][hapmap]
rs1984750	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2288409	1.00[JPT][hapmap]
rs2288410	1.00[JPT][hapmap]
rs2303685	1.00[JPT][hapmap]
rs2560871	1.00[JPT][hapmap]
rs4458121	1.00[JPT][hapmap]
rs61435553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259175	1.00[JPT][hapmap]
rs73935026	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755531	1.00[JPT][hapmap]
rs8100048	1.00[JPT][hapmap]
rs8101364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101990	1.00[JPT][hapmap]
rs8103874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106271	1.00[JPT][hapmap]
rs8107377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108636	1.00[JPT][hapmap]
rs8110857	1.00[JPT][hapmap]
rs8110881	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16983548	PPP2R1A	cis	multi-tissue	Pritchard
rs16983548	PPP2R1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52694400-52710200	ZNF genes & repeats	A549	lung
2	chr19:52694600-52702600	Weak transcription	Aorta	Aorta
3	chr19:52694600-52732800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:52695200-52701200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:52695200-52702000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:52695200-52702800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:52695200-52708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:52695200-52711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:52695400-52701800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:52695400-52702800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:52695400-52702800	Strong transcription	NHLF	lung
12	chr19:52695400-52707600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:52695400-52732200	Strong transcription	Fetal Lung	lung
14	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:52695600-52702200	Strong transcription	HSMM	muscle
16	chr19:52695600-52702400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr19:52695600-52702600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:52695600-52717400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr19:52695800-52701200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:52696000-52701400	Strong transcription	NHEK	skin
21	chr19:52696000-52701400	Strong transcription	Osteobl	bone
22	chr19:52696000-52710800	Strong transcription	Thymus	Thymus
23	chr19:52696000-52723000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr19:52696000-52732200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:52696000-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:52696000-52733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:52696200-52701400	Strong transcription	Placenta	Placenta
28	chr19:52696200-52701400	Strong transcription	NHDF-Ad	bronchial
29	chr19:52696200-52702200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:52696200-52704600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:52696200-52705200	Weak transcription	Small Intestine	intestine
32	chr19:52696200-52729200	Strong transcription	Fetal Intestine Large	intestine
33	chr19:52696200-52732400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:52696200-52732400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:52696200-52732400	Strong transcription	Primary B cells from cord blood	blood
36	chr19:52696600-52701200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:52696600-52701400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:52696600-52702000	Strong transcription	Fetal Intestine Small	intestine
39	chr19:52696600-52702200	Strong transcription	Fetal Stomach	stomach
40	chr19:52696600-52703200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:52696800-52701200	Weak transcription	Fetal Kidney	kidney
42	chr19:52696800-52705600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:52697400-52701600	Genic enhancers	Left Ventricle	heart
44	chr19:52697600-52701400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:52697600-52702000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:52697600-52702000	Strong transcription	Brain Germinal Matrix	brain
47	chr19:52697600-52732400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:52697800-52701800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr19:52697800-52702000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links