Variant report

Variant	rs4858664
Chromosome Location	chr3:19991482-19991483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:19991431-19991487	ProgFib	skin:	n/a	n/a
2	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
3	POLR2A	chr3:19991354-19991502	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
3	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
4	chr3:19991110..19993492-chr3:20053410..20056377,2	K562	blood:
5	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

No data

Variant related genes	Relation type
EFHB	TF binding region
RAB5A	TF binding region
ENSG00000229468	Chromatin interaction
ENSG00000183977	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000129810	Chromatin interaction

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

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

rs_ID	r²[population]
rs10510497	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374092	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486167	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486526	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488378	1.00[ASN][1000 genomes]
rs12490848	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495866	0.91[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796230	1.00[AFR][1000 genomes];0.96[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	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241539	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398451	1.00[ASN][1000 genomes]
rs45542931	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858632	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858662	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858674	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55892327	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56029370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241285	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241286	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62241289	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241316	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241322	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241330	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241333	1.00[ASN][1000 genomes]
rs62241334	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241337	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];0.98[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	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:19988200-19991600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:19988200-19991600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:19989800-19991800	Weak transcription	Small Intestine	intestine
6	chr3:19989800-19993000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:19989800-19993000	Weak transcription	Esophagus	oesophagus
8	chr3:19989800-19993000	Weak transcription	Spleen	Spleen
9	chr3:19989800-19995000	Weak transcription	Gastric	stomach
10	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:19990000-19991800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:19990000-19991800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:19990000-19991800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:19990000-19991800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:19990000-19992600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:19990000-19993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:19990200-19991600	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:19990200-19991600	Enhancers	Stomach Mucosa	stomach
21	chr3:19990200-19992000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:19990200-19992200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:19990400-19991600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr3:19990400-19992000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:19990600-19991600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:19990600-19991600	Genic enhancers	Fetal Intestine Small	intestine
27	chr3:19990600-19991600	Enhancers	Placenta	Placenta
28	chr3:19990600-19992200	Enhancers	Liver	Liver
29	chr3:19990800-19991600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:19990800-19991600	Enhancers	Left Ventricle	heart
31	chr3:19990800-19991600	Enhancers	Ovary	ovary
32	chr3:19990800-19991600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:19990800-19991600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr3:19990800-19991600	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr3:19990800-19991800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:19990800-19992000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:19990800-19992000	Enhancers	Fetal Muscle Leg	muscle
38	chr3:19990800-19992000	Enhancers	Pancreas	Pancrea
39	chr3:19990800-19992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:19990800-19993000	Weak transcription	Fetal Stomach	stomach
41	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
43	chr3:19991000-19991600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:19991000-19991600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:19991000-19991600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:19991000-19991600	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:19991000-19991600	Enhancers	Psoas Muscle	Psoas
48	chr3:19991000-19991600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:19991000-19991600	Weak transcription	NH-A	brain
50	chr3:19991000-19991800	Enhancers	Dnd41	blood

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