Variant report

Variant	rs1041159
Chromosome Location	chr1:92076523-92076524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92067249..92070219-chr1:92074709..92076906,3	K562	blood:
2	chr1:92067249..92070219-chr1:92074709..92076665,2	K562	blood:
3	chr1:92076490..92078813-chr1:92209944..92211883,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1041160	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782974	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10782975	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874824	0.85[ASN][1000 genomes]
rs10874830	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874833	0.82[AMR][1000 genomes]
rs11165071	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165072	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800345	0.83[ASN][1000 genomes]
rs1192404	0.96[ASN][1000 genomes]
rs1192408	0.95[ASN][1000 genomes]
rs1192411	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1192413	0.90[ASN][1000 genomes]
rs1192414	1.00[ASN][1000 genomes]
rs1192415	1.00[ASN][1000 genomes]
rs1192419	1.00[ASN][1000 genomes]
rs12028715	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028723	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12031478	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032884	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033679	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036943	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037771	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122877	0.82[ASN][1000 genomes]
rs12124960	0.83[ASN][1000 genomes]
rs2136115	1.00[ASN][1000 genomes]
rs2136116	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840239	1.00[ASN][1000 genomes]
rs35308020	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370265	0.83[EUR][1000 genomes]
rs4658101	1.00[ASN][1000 genomes]
rs4658103	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658246	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658247	0.81[EUR][1000 genomes]
rs6604047	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604048	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604049	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671034	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981554	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1041159	TGFBR3	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92068200-92083800	Weak transcription	Fetal Lung	lung
2	chr1:92072600-92077600	Weak transcription	Ovary	ovary
3	chr1:92073400-92078000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:92073400-92078200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:92073800-92079400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:92074000-92080000	Enhancers	NHDF-Ad	bronchial
7	chr1:92074200-92077600	Enhancers	NHEK	skin
8	chr1:92074200-92077800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:92074400-92076600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:92074400-92076600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:92074400-92078200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:92074400-92078200	Enhancers	Placenta	Placenta
13	chr1:92074400-92078800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:92074600-92078200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:92074800-92078000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:92074800-92080000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:92075000-92077400	Enhancers	K562	blood
18	chr1:92075200-92078000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:92075400-92076600	Enhancers	NHLF	lung
20	chr1:92075400-92078000	Enhancers	Fetal Muscle Leg	muscle
21	chr1:92075400-92079400	Weak transcription	Fetal Heart	heart
22	chr1:92075800-92078200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:92075800-92079000	Weak transcription	HSMMtube	muscle
24	chr1:92075800-92079200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:92075800-92079400	Enhancers	A549	lung
26	chr1:92075800-92088200	Weak transcription	Right Atrium	heart
27	chr1:92076000-92077000	Weak transcription	NH-A	brain
28	chr1:92076000-92077200	Weak transcription	Osteobl	bone
29	chr1:92076200-92076600	Flanking Active TSS	Hela-S3	cervix
30	chr1:92076200-92078000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:92076200-92078600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:92076200-92079200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:92076200-92079200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:92076400-92076600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:92076400-92076600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:92076400-92077200	Weak transcription	Stomach Mucosa	stomach
37	chr1:92076400-92078000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr1:92076400-92078800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:92076400-92079000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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