Variant report

Variant	rs12151243
Chromosome Location	chr19:40862872-40862873
allele	G/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	chr19:40861809-40862962	GM12891	blood:	n/a	n/a
2	STAT5A	chr19:40862363-40862940	GM12878	blood:	n/a	chr19:40862638-40862650

No.	Distal block	Cell Line	Cell type
1	chr19:40861491..40863430-chr19:40866543..40869308,2	K562	blood:
2	chr19:40853920..40856703-chr19:40862603..40866302,4	K562	blood:
3	chr19:40854582..40856444-chr19:40862603..40865437,3	K562	blood:
4	chr19:40858935..40867508-chr19:40870167..40875772,11	K562	blood:

Variant related genes	Relation type
PLD3	TF binding region
ENSG00000160392	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10408356	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10415181	0.85[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs10416620	0.89[EUR][1000 genomes]
rs10418932	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs10419465	0.89[EUR][1000 genomes]
rs10420842	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422343	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10423896	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16974157	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs2304188	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap]
rs28667591	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34716810	0.89[EUR][1000 genomes]
rs55862427	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57804337	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs57885763	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58336440	0.90[EUR][1000 genomes]
rs58613082	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59010363	0.90[EUR][1000 genomes]
rs60869669	0.90[EUR][1000 genomes]
rs61685259	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62107590	0.90[EUR][1000 genomes]
rs62107593	0.89[EUR][1000 genomes]
rs62107594	0.89[EUR][1000 genomes]
rs62107630	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62107631	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247916	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7248012	0.83[ASN][1000 genomes]
rs7248861	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7254617	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs8100207	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111619	0.88[EUR][1000 genomes]
rs8112998	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs892118	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs892119	0.91[EUR][1000 genomes]
rs892120	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs9304588	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9304589	0.90[EUR][1000 genomes]
rs934426	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers 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 lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12151243	APOC4	cis	cerebellum	SCAN
rs12151243	EML2	cis	cerebellum	SCAN
rs12151243	DEDD2	cis	cerebellum	SCAN
rs12151243	RPL18	cis	parietal	SCAN
rs12151243	PSG8	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40855400-40864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr19:40855600-40863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:40855600-40863200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr19:40855600-40863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:40855600-40863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:40855600-40863600	Weak transcription	Fetal Brain Female	brain
7	chr19:40855600-40863800	Weak transcription	Liver	Liver
8	chr19:40855600-40864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:40855600-40864000	Weak transcription	Spleen	Spleen
10	chr19:40855600-40864000	Weak transcription	NH-A	brain
11	chr19:40855600-40864400	Weak transcription	Placenta	Placenta
12	chr19:40855600-40865200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:40855600-40865200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:40855600-40865200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:40855600-40865200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:40855600-40865200	Weak transcription	Thymus	Thymus
17	chr19:40855600-40865200	Weak transcription	A549	lung
18	chr19:40855600-40865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:40855600-40865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:40855600-40865400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:40855600-40865800	Weak transcription	K562	blood
22	chr19:40855600-40866000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:40855600-40866200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:40855600-40866200	Weak transcription	Esophagus	oesophagus
25	chr19:40855600-40866600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:40855600-40868800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:40855600-40868800	Weak transcription	HSMM	muscle
28	chr19:40855600-40869000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr19:40855600-40869000	Weak transcription	Osteobl	bone
30	chr19:40855600-40870600	Weak transcription	Gastric	stomach
31	chr19:40855600-40870800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:40855600-40870800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:40855600-40870800	Weak transcription	Hela-S3	cervix
34	chr19:40855600-40871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:40855600-40871000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:40855600-40871000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:40855600-40871000	Weak transcription	Fetal Brain Male	brain
38	chr19:40855600-40871000	Weak transcription	Fetal Intestine Large	intestine
39	chr19:40855600-40871000	Weak transcription	Right Atrium	heart
40	chr19:40855600-40871000	Weak transcription	NHDF-Ad	bronchial
41	chr19:40855600-40871000	Weak transcription	NHEK	skin
42	chr19:40855600-40871200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:40855600-40871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:40855600-40871200	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:40855600-40871200	Weak transcription	Small Intestine	intestine
46	chr19:40855600-40871400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:40855600-40871400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:40855600-40871400	Weak transcription	Left Ventricle	heart
49	chr19:40855600-40871400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr19:40855600-40871400	Weak transcription	Rectal Smooth Muscle	rectum

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