Variant report

Variant	rs2457798
Chromosome Location	chr19:22002611-22002612
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10407896	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414358	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463314	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12609186	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1877130	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2435036	0.87[ASN][1000 genomes]
rs2435039	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2435049	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457784	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457792	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2457794	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2457800	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075276	0.87[ASN][1000 genomes]
rs4809179	0.80[JPT][hapmap]
rs7247610	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	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	nsv578971	chr19:21950337-22008229	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2457798	ZNF100	cis	parietal	SCAN
rs2457798	ZNF100	cis	cerebellum	SCAN
rs2457798	RP11-420K14.3	cis	lung	GTEx
rs2457798	RP11-420K14.3	cis	Esophagus Muscularis	GTEx
rs2457798	ZNF100	cis	Nerve Tibial	GTEx
rs2457798	VN1R84P	cis	lung	GTEx
rs2457798	ZNF100	cis	Adipose Subcutaneous	GTEx
rs2457798	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs2457798	ZNF100	cis	Esophagus Muscularis	GTEx
rs2457798	ZNF100	cis	Artery Tibial	GTEx
rs2457798	RP11-420K14.3	cis	Whole Blood	GTEx
rs2457798	ZNF100	cis	Muscle Skeletal	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21985400-22003000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21985600-22011000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21987800-22002800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:21988600-22018000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:21988800-22003000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:21988800-22017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21989600-22002800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr19:21989600-22002800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr19:21989800-22013000	ZNF genes & repeats	Brain Germinal Matrix	brain
10	chr19:21990000-22005200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:21990400-22002800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr19:21990400-22002800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr19:21991000-22003800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:21991200-22010800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:21993800-22003400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:21994200-22002800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:21995000-22016600	Weak transcription	K562	blood
19	chr19:21998600-22003000	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr19:21999800-22003800	Weak transcription	Stomach Mucosa	stomach
21	chr19:21999800-22008400	Weak transcription	Right Ventricle	heart
22	chr19:21999800-22009000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:21999800-22009400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:21999800-22018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:22000800-22003600	Weak transcription	HSMMtube	muscle
26	chr19:22000800-22004000	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:22000800-22007800	Weak transcription	Fetal Kidney	kidney
28	chr19:22000800-22008200	Weak transcription	HSMM	muscle
29	chr19:22000800-22008400	Weak transcription	Placenta	Placenta
30	chr19:22000800-22018200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:22000800-22018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:22001000-22004400	Weak transcription	NHEK	skin
33	chr19:22001000-22008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:22001000-22012600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr19:22001000-22014000	Weak transcription	Psoas Muscle	Psoas
36	chr19:22001000-22018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:22001000-22018000	Weak transcription	Brain Anterior Caudate	brain
38	chr19:22001000-22018000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:22001200-22004200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:22001200-22009200	Weak transcription	Pancreas	Pancrea
41	chr19:22001200-22018200	Weak transcription	Gastric	stomach
42	chr19:22001400-22004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:22001400-22006400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:22001400-22009200	Weak transcription	Spleen	Spleen
45	chr19:22001400-22012600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:22001600-22002800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr19:22001600-22002800	ZNF genes & repeats	Dnd41	blood
48	chr19:22001600-22004800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:22001600-22008400	Weak transcription	Ovary	ovary
50	chr19:22001600-22008600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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