Variant report

Variant	rs2457789
Chromosome Location	chr19:22024004-22024005
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	CEBPB	chr19:22023961-22024697	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:22022147-22024612	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr19:22023936-22024736	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-7	chr19:22022399-22024449	NONHSAT063748

Variant related genes	Relation type
ZNF43	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1510964	1.00[YRI][hapmap]
rs1543048	1.00[ASN][1000 genomes]
rs16998303	1.00[CHB][hapmap]
rs16998391	1.00[ASN][1000 genomes]
rs16998411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2203944	1.00[CHB][hapmap]
rs2244041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359707	1.00[ASN][1000 genomes]
rs2435001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435041	1.00[YRI][hapmap]
rs2435044	1.00[YRI][hapmap]
rs2435045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435046	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457785	0.97[MKK][hapmap];0.88[YRI][hapmap]
rs2457787	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457793	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457795	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467196	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6511296	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription 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	23 gene(s)	inside rSNPs	diseases
6	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3395280	chr19:21968753-22202288	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv911428	chr19:21986292-22106951	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv911429	chr19:21986292-22110219	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv911430	chr19:22008229-22106951	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1062497	chr19:22013911-22102714	Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv543949	chr19:22013911-22102714	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv917200	chr19:22020157-22101914	Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2457789	GPR3	trans	brain	seeQTL
rs2457789	HBG2	trans	brain	seeQTL
rs2457789	HBG1	trans	brain	seeQTL
rs2457789	LAMB3	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22019000-22024800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:22019000-22027800	Weak transcription	Small Intestine	intestine
3	chr19:22019000-22034200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:22019200-22025600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:22019200-22034000	Weak transcription	Colonic Mucosa	Colon
6	chr19:22019200-22034400	Weak transcription	Stomach Mucosa	stomach
7	chr19:22019400-22033600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:22019600-22024200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:22019600-22024400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:22019600-22024600	Weak transcription	Right Ventricle	heart
11	chr19:22019600-22025600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:22019600-22025600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:22019600-22025800	Weak transcription	Fetal Brain Male	brain
14	chr19:22019600-22026200	Weak transcription	Psoas Muscle	Psoas
15	chr19:22019600-22032800	Weak transcription	Right Atrium	heart
16	chr19:22019600-22033400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:22019600-22033600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:22019800-22025400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:22019800-22028000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:22019800-22033600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:22020000-22032600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:22020200-22027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:22020400-22032600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr19:22020400-22032600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:22020400-22032600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:22020400-22033400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:22020400-22033400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:22020600-22033400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:22020600-22033400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:22021000-22025800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:22021200-22031600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:22021200-22032400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:22021200-22032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:22021400-22029600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:22021400-22029600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:22021400-22033000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:22021600-22024400	Strong transcription	NHDF-Ad	bronchial
38	chr19:22021600-22026800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:22021600-22028200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:22021600-22029000	Strong transcription	Brain Germinal Matrix	brain
41	chr19:22021600-22030200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr19:22021600-22031800	Strong transcription	Primary B cells from cord blood	blood
43	chr19:22021600-22032000	Strong transcription	Thymus	Thymus
44	chr19:22021600-22032400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:22021600-22032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:22021600-22032600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:22021600-22032600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:22021600-22033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:22021600-22033600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr19:22021600-22033600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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