Variant report

Variant	rs4658101
Chromosome Location	chr1:92077409-92077410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92076490..92078813-chr1:92209944..92211883,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1041159	1.00[ASN][1000 genomes]
rs1041160	0.97[ASN][1000 genomes]
rs10782975	1.00[ASN][1000 genomes]
rs10874824	0.85[ASN][1000 genomes]
rs10874830	1.00[ASN][1000 genomes]
rs11165071	1.00[ASN][1000 genomes]
rs11165072	1.00[ASN][1000 genomes]
rs11800345	0.83[ASN][1000 genomes]
rs1192404	0.96[ASN][1000 genomes]
rs1192408	0.95[ASN][1000 genomes]
rs1192411	0.94[ASN][1000 genomes]
rs1192413	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1192414	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192415	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1192419	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028715	1.00[ASN][1000 genomes]
rs12028723	0.96[ASN][1000 genomes]
rs12031478	1.00[ASN][1000 genomes]
rs12032884	1.00[ASN][1000 genomes]
rs12033679	1.00[ASN][1000 genomes]
rs12036943	0.92[ASN][1000 genomes]
rs12037771	1.00[ASN][1000 genomes]
rs12122877	0.82[ASN][1000 genomes]
rs12124960	0.83[ASN][1000 genomes]
rs2136115	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136116	1.00[ASN][1000 genomes]
rs2174951	1.00[ASN][1000 genomes]
rs2840239	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35308020	1.00[ASN][1000 genomes]
rs4658103	1.00[ASN][1000 genomes]
rs4658246	1.00[ASN][1000 genomes]
rs6604047	0.97[ASN][1000 genomes]
rs6604048	0.97[ASN][1000 genomes]
rs6604049	0.97[ASN][1000 genomes]
rs6671034	0.96[ASN][1000 genomes]
rs981554	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

Variant related diseases (count:1)

Disease	PMID	Source
Vertical cup-disc ratio	25241763	GWAS catalog

Chromatin state (count:49 , 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	chr1:92074400-92078200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:92074400-92078200	Enhancers	Placenta	Placenta
11	chr1:92074400-92078800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:92074600-92078200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:92074800-92078000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:92074800-92080000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:92075200-92078000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:92075400-92078000	Enhancers	Fetal Muscle Leg	muscle
17	chr1:92075400-92079400	Weak transcription	Fetal Heart	heart
18	chr1:92075800-92078200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:92075800-92079000	Weak transcription	HSMMtube	muscle
20	chr1:92075800-92079200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:92075800-92079400	Enhancers	A549	lung
22	chr1:92075800-92088200	Weak transcription	Right Atrium	heart
23	chr1:92076200-92078000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:92076200-92078600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:92076200-92079200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:92076200-92079200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:92076400-92078000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr1:92076400-92078800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:92076400-92079000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:92076600-92077600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:92076600-92077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:92076600-92077800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:92076800-92078200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:92077000-92077600	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:92077000-92077800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:92077000-92077800	Flanking Active TSS	Hela-S3	cervix
37	chr1:92077000-92078000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:92077200-92077800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr1:92077200-92077800	Enhancers	Stomach Mucosa	stomach
40	chr1:92077200-92078000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:92077200-92078000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:92077200-92078000	Enhancers	Colonic Mucosa	Colon
43	chr1:92077200-92078000	Enhancers	Fetal Stomach	stomach
44	chr1:92077200-92078000	Enhancers	Lung	lung
45	chr1:92077200-92079200	Weak transcription	NHLF	lung
46	chr1:92077400-92079200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:92077400-92079400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:92077400-92082800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:92077400-92082800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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