Variant report

Variant	rs10407896
Chromosome Location	chr19:22019444-22019445
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:22018206-22019476	HUVEC	blood vessel:	n/a	n/a
2	MAFK	chr19:22018604-22019502	H1-hESC	embryonic stem cell:	n/a	n/a
3	TBP	chr19:22018444-22019499	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:22018148-22019724	PANC-1	pancreas:	n/a	n/a
5	SIN3A	chr19:22018473-22019464	H1-hESC	embryonic stem cell:	n/a	chr19:22018629-22018640
6	CHD2	chr19:22018471-22019478	K562	blood:	n/a	n/a
7	POLR2A	chr19:22018080-22019600	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:22019388-22019541	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:22018262-22019645	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:22018125-22019654	K562	blood:	n/a	n/a
11	POLR2A	chr19:22018084-22019568	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:22018015-22019648	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:22018354-22019499	GM18951	blood:	n/a	n/a
14	MAFF	chr19:22019390-22019618	K562	blood:	n/a	n/a
15	POLR2A	chr19:22017902-22019672	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:22018238-22019639	PFSK-1	brain:	n/a	n/a
17	MXI1	chr19:22018336-22019859	SK-N-SH	brain:	n/a	n/a
18	MYC	chr19:22018570-22019540	NB4	blood:	n/a	n/a
19	MYC	chr19:22018560-22019555	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr19:22018086-22019788	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr19:22018043-22019678	PANC-1	pancreas:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21948493..21950510-chr19:22018479..22020127,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF43	TF binding region
ENSG00000197020	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10414358	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12463314	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12609186	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877130	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2244127	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435000	0.89[AFR][1000 genomes]
rs2435036	0.89[ASN][1000 genomes]
rs2435039	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2435049	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2457784	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457792	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457794	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457798	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2457800	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075276	0.88[ASN][1000 genomes]
rs7247610	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking 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	13 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv961194	chr19:21998424-22019912	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	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
15	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
16	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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10407896	ZNF100	cis	Esophagus Muscularis	GTEx
rs10407896	ZNF100	cis	Artery Tibial	GTEx
rs10407896	ZNF100	cis	lung	GTEx
rs10407896	ZNF100	cis	Muscle Skeletal	GTEx
rs10407896	ZNF100	Cis_1M	lymphoblastoid	RTeQTL
rs10407896	ZNF100	cis	Nerve Tibial	GTEx
rs10407896	VN1R84P	cis	Nerve Tibial	GTEx
rs10407896	ZNF100	cis	Adipose Subcutaneous	GTEx
rs10407896	VN1R84P	cis	lung	GTEx
rs10407896	RP11-420K14.3	cis	Whole Blood	GTEx
rs10407896	RP11-420K14.3	cis	lung	GTEx
rs10407896	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs10407896	RP11-420K14.3	cis	Esophagus Muscularis	GTEx
rs10407896	ZNF100	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22017800-22019600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:22017800-22019600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr19:22017800-22019600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:22018000-22019600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:22018000-22019600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:22018000-22019600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:22018000-22019600	Active TSS	Fetal Brain Female	brain
8	chr19:22018200-22019600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:22019000-22019600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:22019000-22019600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:22019000-22020400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:22019000-22020600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:22019000-22021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:22019000-22021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:22019000-22021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:22019000-22022200	Weak transcription	Spleen	Spleen
17	chr19:22019000-22022400	Weak transcription	Lung	lung
18	chr19:22019000-22022600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:22019000-22022600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:22019000-22022800	Weak transcription	Gastric	stomach
21	chr19:22019000-22024800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:22019000-22027800	Weak transcription	Small Intestine	intestine
23	chr19:22019000-22034200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr19:22019200-22019600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:22019200-22019600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:22019200-22019600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:22019200-22019600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:22019200-22019600	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr19:22019200-22019600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr19:22019200-22019600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:22019200-22019600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:22019200-22019600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr19:22019200-22019600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:22019200-22019600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr19:22019200-22019600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:22019200-22019600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:22019200-22019600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:22019200-22019600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:22019200-22019600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:22019200-22019600	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr19:22019200-22019600	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr19:22019200-22019600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr19:22019200-22019600	Flanking Active TSS	Fetal Kidney	kidney
44	chr19:22019200-22019600	Enhancers	Placenta	Placenta
45	chr19:22019200-22019600	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr19:22019200-22019600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr19:22019200-22019600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr19:22019200-22019600	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr19:22019200-22019600	Flanking Active TSS	Dnd41	blood
50	chr19:22019200-22019600	Enhancers	Osteobl	bone

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