Variant report

Variant	rs1192404
Chromosome Location	chr1:92068967-92068968
allele	A/G
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..92076665,2	K562	blood:
2	chr1:92067249..92070219-chr1:92074709..92076906,3	K562	blood:
3	chr1:92059728..92061441-chr1:92068842..92071690,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1041159	0.96[ASN][1000 genomes]
rs1041160	0.94[ASN][1000 genomes]
rs10493852	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10782975	0.96[ASN][1000 genomes]
rs10874824	0.88[ASN][1000 genomes]
rs10874830	0.96[ASN][1000 genomes]
rs11165071	0.96[ASN][1000 genomes]
rs11165072	0.96[ASN][1000 genomes]
rs11800345	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1192408	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192411	0.95[ASN][1000 genomes]
rs1192413	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1192414	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1192415	0.96[ASN][1000 genomes]
rs1192419	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12028715	0.96[ASN][1000 genomes]
rs12028723	0.92[ASN][1000 genomes]
rs12031478	0.96[ASN][1000 genomes]
rs12032884	0.96[ASN][1000 genomes]
rs12033679	0.96[ASN][1000 genomes]
rs12036943	0.88[ASN][1000 genomes]
rs12037771	0.96[ASN][1000 genomes]
rs12122877	0.85[ASN][1000 genomes]
rs12122935	0.83[ASN][1000 genomes]
rs12124960	0.86[ASN][1000 genomes]
rs2136115	0.96[ASN][1000 genomes]
rs2136116	0.96[ASN][1000 genomes]
rs2174951	0.96[ASN][1000 genomes]
rs2840239	0.96[ASN][1000 genomes]
rs35308020	0.96[ASN][1000 genomes]
rs4658101	0.96[ASN][1000 genomes]
rs4658103	0.96[ASN][1000 genomes]
rs4658246	0.96[ASN][1000 genomes]
rs6604047	0.94[ASN][1000 genomes]
rs6604048	0.94[ASN][1000 genomes]
rs6604049	0.94[ASN][1000 genomes]
rs6671034	0.92[ASN][1000 genomes]
rs6693314	0.84[EUR][1000 genomes]
rs981554	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv947497	chr1:92067233-92076450	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1192404	RPAP2	cis	cerebellum	SCAN
rs1192404	RPAP2	cis	parietal	SCAN
rs1192404	TGFBR3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92055800-92076400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:92057200-92070400	Weak transcription	Psoas Muscle	Psoas
3	chr1:92060600-92070200	Weak transcription	Right Ventricle	heart
4	chr1:92060800-92070200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:92061200-92070000	Weak transcription	Ovary	ovary
6	chr1:92062400-92074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:92064000-92070000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:92066000-92069200	Enhancers	NHDF-Ad	bronchial
9	chr1:92066400-92069000	Weak transcription	Fetal Kidney	kidney
10	chr1:92066800-92069000	Weak transcription	Right Atrium	heart
11	chr1:92067600-92071600	Weak transcription	Spleen	Spleen
12	chr1:92067800-92070000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:92067800-92070400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:92068000-92069000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:92068200-92070000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:92068200-92070000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:92068200-92070000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:92068200-92070000	Weak transcription	Fetal Stomach	stomach
19	chr1:92068200-92070000	Weak transcription	Left Ventricle	heart
20	chr1:92068200-92071800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:92068200-92083800	Weak transcription	Fetal Lung	lung
22	chr1:92068400-92069400	Weak transcription	Fetal Heart	heart
23	chr1:92068400-92070200	Weak transcription	Adipose Nuclei	Adipose
24	chr1:92068600-92070000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:92068600-92070000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:92068800-92069600	Enhancers	GM12878-XiMat	blood
27	chr1:92068800-92070000	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:92068800-92074400	Weak transcription	Placenta	Placenta

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