Variant report

Variant	rs3784244
Chromosome Location	chr14:20780367-20780368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1000608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1057605	0.87[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1132644	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11845291	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11848535	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12588213	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12889262	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890140	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1713418	0.83[MEX][hapmap]
rs1713419	0.83[MEX][hapmap]
rs1889361	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1953549	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1953552	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001572	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28500547	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4451865	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981975	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6575132	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6575164	0.85[CEU][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap]
rs7159947	0.91[LWK][hapmap]
rs7160770	0.92[ASW][hapmap];0.85[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers 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	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3784244	RPPH1	cis	parietal	SCAN
rs3784244	PARP2	cis	cerebellum	SCAN
rs3784244	PARP2	cis	parietal	SCAN
rs3784244	CCNB1IP1	cis	cerebellum	SCAN
rs3784244	PRMT5	cis	parietal	SCAN
rs3784244	CCNB1IP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20774200-20780400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr14:20774200-20780600	Weak transcription	Colonic Mucosa	Colon
3	chr14:20774200-20780600	Weak transcription	Hela-S3	cervix
4	chr14:20774200-20780800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr14:20774200-20780800	Weak transcription	NHLF	lung
6	chr14:20774200-20781000	Weak transcription	Primary T cells from cord blood	blood
7	chr14:20774200-20781000	Weak transcription	Fetal Lung	lung
8	chr14:20774200-20781200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr14:20774200-20781200	Weak transcription	Placenta	Placenta
10	chr14:20774200-20781400	Weak transcription	Primary B cells from cord blood	blood
11	chr14:20774200-20781400	Weak transcription	Esophagus	oesophagus
12	chr14:20774200-20781400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:20774200-20781400	Weak transcription	Psoas Muscle	Psoas
14	chr14:20774200-20781600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:20774200-20781600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:20774200-20784000	Weak transcription	Fetal Intestine Small	intestine
17	chr14:20774200-20784000	Weak transcription	Right Ventricle	heart
18	chr14:20774200-20784400	Weak transcription	Aorta	Aorta
19	chr14:20774200-20785000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr14:20774200-20785000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr14:20774200-20785400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr14:20774200-20785400	Weak transcription	Thymus	Thymus
23	chr14:20774200-20785400	Weak transcription	Spleen	Spleen
24	chr14:20774200-20785600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr14:20774200-20785800	Weak transcription	Gastric	stomach
26	chr14:20774200-20786000	Weak transcription	Pancreas	Pancrea
27	chr14:20774200-20795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr14:20774200-20795600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr14:20774200-20795600	Weak transcription	Fetal Heart	heart
30	chr14:20774200-20800400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr14:20774200-20800400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:20774200-20800400	Weak transcription	Fetal Brain Male	brain
33	chr14:20774200-20800400	Weak transcription	Stomach Mucosa	stomach
34	chr14:20774200-20800600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr14:20774200-20800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr14:20774200-20800800	Weak transcription	Small Intestine	intestine
37	chr14:20774400-20780600	Weak transcription	Brain Angular Gyrus	brain
38	chr14:20774400-20781400	Weak transcription	Brain Anterior Caudate	brain
39	chr14:20774400-20781400	Weak transcription	Brain Hippocampus Middle	brain
40	chr14:20774400-20781400	Weak transcription	Brain Substantia Nigra	brain
41	chr14:20774400-20781400	Weak transcription	Fetal Brain Female	brain
42	chr14:20774400-20784400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr14:20774400-20787200	Weak transcription	Brain Germinal Matrix	brain
44	chr14:20778800-20798600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr14:20779000-20795600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:20779400-20780400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr14:20779400-20781800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:20779400-20782200	Strong transcription	Fetal Stomach	stomach
49	chr14:20779400-20787000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr14:20779400-20788400	Strong transcription	Duodenum Mucosa	Duodenum

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