Variant report

Variant	rs4858662
Chromosome Location	chr3:19993703-19993704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19992532..19994138-chr3:20013293..20015192,2	K562	blood:
2	chr3:19971502..19973500-chr3:19993301..19994870,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510497	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[ASN][1000 genomes]
rs12490848	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497549	1.00[ASN][1000 genomes]
rs17181337	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365374	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28597881	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241539	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398451	1.00[ASN][1000 genomes]
rs45542931	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858664	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241279	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62243065	1.00[ASN][1000 genomes]
rs62243074	1.00[ASN][1000 genomes]
rs62243075	1.00[ASN][1000 genomes]
rs62243076	1.00[ASN][1000 genomes]
rs73032477	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034166	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-19995000	Weak transcription	Gastric	stomach
2	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
7	chr3:19991000-19995200	Weak transcription	Brain Germinal Matrix	brain
8	chr3:19991000-19996200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:19991000-19996600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
12	chr3:19991400-19993800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:19991400-19995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:19991400-19995400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:19991400-19995400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:19991400-19998200	Weak transcription	Aorta	Aorta
17	chr3:19991400-19998800	Strong transcription	Fetal Thymus	thymus
18	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:19991600-19995000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:19991600-19995400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:19991600-19997200	Strong transcription	NH-A	brain
22	chr3:19991600-19998400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:19991600-19998400	Weak transcription	Psoas Muscle	Psoas
24	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:19991800-19994400	Strong transcription	Fetal Lung	lung
27	chr3:19991800-19994600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:19991800-19997600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:19991800-19998000	Strong transcription	Fetal Intestine Large	intestine
30	chr3:19992000-19994200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr3:19992000-19994200	Strong transcription	Hela-S3	cervix
32	chr3:19992000-19994400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:19992000-19994600	Strong transcription	Brain Substantia Nigra	brain
34	chr3:19992000-19995400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:19992000-19995600	Weak transcription	Pancreas	Pancrea
36	chr3:19992000-19996200	Weak transcription	NHDF-Ad	bronchial
37	chr3:19992000-19998200	Strong transcription	K562	blood
38	chr3:19992000-20000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:19992000-20000200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:19992200-19994000	Genic enhancers	Liver	Liver
44	chr3:19992200-19994600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:19992200-19996600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:19992200-19998400	Strong transcription	Placenta	Placenta
47	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
49	chr3:19992400-19993800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:19992400-19993800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--

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