Variant report

Variant	rs16983557
Chromosome Location	chr19:52708771-52708772
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52641137..52643378-chr19:52708305..52710769,2	MCF-7	breast:
2	chr19:52708640..52710862-chr19:52712788..52715037,2	K562	blood:
3	chr19:52693832..52696719-chr19:52708763..52711049,3	MCF-7	breast:
4	chr19:52707646..52710337-chr19:52740110..52742773,2	K562	blood:
5	chr19:52707197..52709846-chr19:52723808..52726393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105568	Chromatin interaction
ENSG00000204611	Chromatin interaction

Extended variants
information (count: 69 )
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];0.93[AMR][1000 genomes];0.98[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];0.87[EUR][1000 genomes]
rs10405856	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10405862	0.87[EUR][1000 genomes]
rs10407502	1.00[JPT][hapmap]
rs10407987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408119	1.00[JPT][hapmap]
rs10410908	0.88[CEU][hapmap]
rs10411335	0.88[CEU][hapmap];0.87[YRI][hapmap]
rs10413274	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10413435	1.00[JPT][hapmap]
rs10413470	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10413847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[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	0.86[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	0.94[AMR][1000 genomes];0.98[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];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424348	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]
rs10425135	1.00[JPT][hapmap]
rs10425393	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426066	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16983548	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]
rs16983549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983598	1.00[JPT][hapmap]
rs16983603	1.00[JPT][hapmap]
rs1984750	0.87[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	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253157	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259175	1.00[JPT][hapmap]
rs73935026	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937434	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755531	1.00[JPT][hapmap]
rs8100048	1.00[JPT][hapmap]
rs8101364	0.90[AMR][1000 genomes];0.98[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16983557	PPP2R1A	Cis_1M	lymphoblastoid	RTeQTL
rs16983557	PPP2R1A	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 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	chr19:52694600-52732800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:52695200-52711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52695400-52732200	Strong transcription	Fetal Lung	lung
5	chr19:52695400-52733200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:52695600-52717400	Strong transcription	Primary hematopoietic stem cells	blood
7	chr19:52696000-52710800	Strong transcription	Thymus	Thymus
8	chr19:52696000-52723000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:52696000-52732200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:52696000-52732400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:52696000-52733000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:52696200-52729200	Strong transcription	Fetal Intestine Large	intestine
13	chr19:52696200-52732400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:52696200-52732400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:52696200-52732400	Strong transcription	Primary B cells from cord blood	blood
16	chr19:52697600-52732400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:52697600-52733200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:52697800-52732200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:52697800-52732400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:52697800-52732400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:52697800-52732600	Strong transcription	Primary T cells from cord blood	blood
22	chr19:52697800-52733000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:52698000-52730400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:52698000-52732200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr19:52698000-52732200	Strong transcription	Dnd41	blood
26	chr19:52698200-52714400	Weak transcription	Stomach Mucosa	stomach
27	chr19:52698200-52732000	Strong transcription	GM12878-XiMat	blood
28	chr19:52698200-52732400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:52698200-52732400	Strong transcription	HepG2	liver
30	chr19:52698200-52732600	Strong transcription	Fetal Brain Female	brain
31	chr19:52698400-52732400	Strong transcription	Fetal Thymus	thymus
32	chr19:52698600-52732000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:52698800-52732400	Strong transcription	Liver	Liver
34	chr19:52700200-52712600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:52700800-52732200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:52702200-52731800	Strong transcription	Primary B cells from peripheral blood	blood
37	chr19:52702200-52732200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr19:52702600-52732200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:52703000-52731600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:52703000-52732600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:52703000-52734600	Strong transcription	Fetal Stomach	stomach
42	chr19:52703200-52709000	Strong transcription	Hela-S3	cervix
43	chr19:52703200-52711000	Strong transcription	Fetal Kidney	kidney
44	chr19:52703200-52711200	Strong transcription	K562	blood
45	chr19:52703200-52714400	Strong transcription	Placenta	Placenta
46	chr19:52703200-52731200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:52703200-52732200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:52703200-52732400	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr19:52703200-52732400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr19:52703200-52732800	Strong transcription	Brain Germinal Matrix	brain

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