Variant report

Variant	rs3730051
Chromosome Location	chr19:40744697-40744698
allele	A/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	REST	chr19:40743359-40746123	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40730680..40732953-chr19:40742312..40745155,2	K562	blood:
2	chr19:40736321..40741961-chr19:40743077..40747922,9	K562	blood:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000105219	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10402740	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]
rs10405207	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1129156	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs11668242	0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs11880261	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs12974529	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12981110	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304184	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs2304189	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339526	0.93[MEX][hapmap]
rs3730050	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4239504	0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs4239506	0.80[AMR][1000 genomes]
rs4257318	0.90[ASW][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs4277441	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4332845	0.81[AMR][1000 genomes]
rs4337402	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs4490099	0.90[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4558508	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4802070	0.85[CHB][hapmap];0.93[MEX][hapmap]
rs4802071	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4802073	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs4802074	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs4803320	1.00[ASW][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508936	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs7249146	0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs7250897	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7257972	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7260517	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs748236	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7508604	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8100018	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs8102171	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs8104727	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8110888	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs969531	1.00[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9749283	0.83[AMR][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	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	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	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
6	nsv1062755	chr19:40737463-40758235	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3730051	C19orf47	cis	multi-tissue	Pritchard
rs3730051	C19orf47	cis	lymphoblastoid	seeQTL
rs3730051	FLJ36888	cis	multi-tissue	Pritchard
rs3730051	ZNF233	cis	cerebellum	SCAN
rs3730051	C19orf47	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40732800-40759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:40735600-40757600	Weak transcription	Stomach Mucosa	stomach
3	chr19:40735800-40748200	Weak transcription	Psoas Muscle	Psoas
4	chr19:40737600-40748600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:40737600-40749600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:40737600-40751200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:40738000-40746600	Strong transcription	Ovary	ovary
8	chr19:40738000-40747000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:40738000-40748600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr19:40738000-40748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:40738000-40749000	Strong transcription	Thymus	Thymus
12	chr19:40738000-40751600	Strong transcription	Dnd41	blood
13	chr19:40738000-40763800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:40738200-40745000	Weak transcription	HSMM	muscle
15	chr19:40738200-40748200	Strong transcription	Pancreas	Pancrea
16	chr19:40738200-40748600	Strong transcription	NHLF	lung
17	chr19:40738200-40748800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr19:40738200-40749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:40738200-40756200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr19:40738400-40745000	Weak transcription	NHDF-Ad	bronchial
21	chr19:40738400-40746800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:40738400-40749400	Strong transcription	Fetal Thymus	thymus
23	chr19:40738400-40749600	Strong transcription	Fetal Brain Female	brain
24	chr19:40738600-40747200	Strong transcription	Brain Cingulate Gyrus	brain
25	chr19:40738600-40747200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:40738600-40747600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:40738600-40747600	Strong transcription	Lung	lung
28	chr19:40738600-40748600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:40738800-40747200	Strong transcription	Brain Hippocampus Middle	brain
30	chr19:40738800-40747600	Weak transcription	Right Atrium	heart
31	chr19:40738800-40748400	Strong transcription	Colonic Mucosa	Colon
32	chr19:40738800-40748600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr19:40738800-40748800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:40738800-40749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:40738800-40750800	Weak transcription	Fetal Heart	heart
36	chr19:40738800-40758000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:40739000-40746400	Strong transcription	Brain Angular Gyrus	brain
38	chr19:40739000-40747400	Strong transcription	Right Ventricle	heart
39	chr19:40739000-40747600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:40739000-40747600	Strong transcription	Brain Germinal Matrix	brain
41	chr19:40739000-40747600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:40739000-40747600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:40739000-40748000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:40739000-40748600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr19:40739000-40748600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:40739000-40748600	Strong transcription	Gastric	stomach
47	chr19:40739000-40749000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:40739000-40749400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:40739000-40751200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:40739200-40747200	Strong transcription	Adipose Nuclei	Adipose

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