Variant report

Variant	rs10874794
Chromosome Location	chr1:92045585-92045586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10458506	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874796	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164978	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165002	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165008	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165013	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048543	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12117800	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4658235	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4658236	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6604044	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604045	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6677520	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs906633	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10874794	RPAP2	cis	cerebellum	SCAN
rs10874794	TGFBR3	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92035800-92047600	Weak transcription	Ovary	ovary
2	chr1:92035800-92048200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:92036400-92051000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:92037200-92045600	Enhancers	Fetal Stomach	stomach
5	chr1:92038200-92049000	Weak transcription	Right Atrium	heart
6	chr1:92039800-92047200	Enhancers	Fetal Heart	heart
7	chr1:92041800-92051200	Weak transcription	Fetal Brain Male	brain
8	chr1:92042000-92048200	Weak transcription	Fetal Kidney	kidney
9	chr1:92042200-92047600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:92042600-92046200	Enhancers	Fetal Lung	lung
11	chr1:92043000-92049000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:92043200-92046200	Enhancers	Colon Smooth Muscle	Colon
13	chr1:92043400-92046000	Enhancers	Rectal Smooth Muscle	rectum
14	chr1:92043400-92046400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:92043800-92046000	Enhancers	K562	blood
16	chr1:92043800-92046000	Enhancers	NHLF	lung
17	chr1:92043800-92047800	Weak transcription	Dnd41	blood
18	chr1:92044200-92046000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:92044200-92047400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:92044400-92046200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:92044400-92048200	Weak transcription	A549	lung
22	chr1:92044600-92045600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr1:92044600-92045600	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:92044600-92047800	Weak transcription	Left Ventricle	heart
25	chr1:92044600-92050000	Weak transcription	Lung	lung
26	chr1:92044800-92047000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:92044800-92048000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:92045000-92045600	Enhancers	Placenta	Placenta
29	chr1:92045000-92049000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:92045200-92046000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:92045400-92045600	Enhancers	NHDF-Ad	bronchial
32	chr1:92045400-92046600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:92045400-92047200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:92045400-92048000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:92045400-92051400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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