Variant report

Variant	rs1574287
Chromosome Location	chr8:19190692-19190693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12334513	0.90[CHB][hapmap]
rs1574288	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116609	0.90[JPT][hapmap]
rs17128221	0.81[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2410609	0.90[JPT][hapmap]
rs35073512	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3824328	0.88[CEU][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4075192	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7829274	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs7845057	0.94[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs9325856	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv917232	chr8:18585309-19208665	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv890616	chr8:18989735-19197809	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
15	nsv890621	chr8:19173379-19211220	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1574287	LZTS1	cis	parietal	SCAN
rs1574287	MTMR7	cis	parietal	SCAN
rs1574287	CNOT7	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19172400-19202400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:19172600-19202800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:19173600-19254800	Weak transcription	Colonic Mucosa	Colon
4	chr8:19173800-19205400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:19174000-19223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:19174200-19191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:19174200-19220400	Weak transcription	HSMM	muscle
8	chr8:19174400-19205200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr8:19178200-19194400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr8:19181800-19204800	Weak transcription	Spleen	Spleen
11	chr8:19183800-19202600	Weak transcription	Primary T cells from cord blood	blood
12	chr8:19184000-19203600	Weak transcription	Small Intestine	intestine
13	chr8:19184400-19191000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:19184400-19196000	Weak transcription	Aorta	Aorta
15	chr8:19185000-19204400	Weak transcription	Fetal Lung	lung
16	chr8:19185400-19190800	Weak transcription	Lung	lung
17	chr8:19186200-19229800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:19186600-19191000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr8:19187200-19198000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:19188000-19190800	Weak transcription	Fetal Intestine Large	intestine
21	chr8:19188000-19191000	Weak transcription	Fetal Kidney	kidney
22	chr8:19188200-19204400	Weak transcription	Right Ventricle	heart
23	chr8:19188400-19202200	Weak transcription	Fetal Heart	heart
24	chr8:19188800-19191000	Weak transcription	Left Ventricle	heart
25	chr8:19189000-19190800	Weak transcription	Gastric	stomach
26	chr8:19189000-19191400	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:19189000-19201600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:19189200-19190800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr8:19189200-19191000	Weak transcription	Esophagus	oesophagus
30	chr8:19189200-19191000	Weak transcription	Stomach Mucosa	stomach
31	chr8:19189400-19190800	Weak transcription	Fetal Stomach	stomach
32	chr8:19189800-19191200	Weak transcription	HMEC	breast
33	chr8:19189800-19197800	Strong transcription	Osteobl	bone
34	chr8:19190000-19198400	Strong transcription	A549	lung
35	chr8:19190200-19197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:19190200-19198000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr8:19190400-19192800	Strong transcription	Fetal Intestine Small	intestine
38	chr8:19190400-19193800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr8:19190400-19193800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr8:19190400-19194400	Strong transcription	HepG2	liver
41	chr8:19190400-19194400	Strong transcription	NHLF	lung
42	chr8:19190400-19194800	Strong transcription	NHDF-Ad	bronchial
43	chr8:19190400-19196200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr8:19190400-19198000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr8:19190400-19198200	Strong transcription	Hela-S3	cervix
46	chr8:19190400-19199000	Strong transcription	Liver	Liver
47	chr8:19190600-19191800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr8:19190600-19191800	Strong transcription	NHEK	skin
49	chr8:19190600-19192400	Strong transcription	Placenta	Placenta
50	chr8:19190600-19192800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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