Variant report

Variant	rs2899054
Chromosome Location	chr4:56921178-56921179
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	chr4:56918589..56921533-chr4:56921686..56923610,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10517367	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1108947	0.86[EUR][1000 genomes]
rs1108948	0.86[EUR][1000 genomes]
rs11721368	0.81[EUR][1000 genomes]
rs11934389	0.86[EUR][1000 genomes]
rs11938852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13102087	0.87[EUR][1000 genomes]
rs13112752	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113844	0.86[EUR][1000 genomes]
rs13121092	0.84[EUR][1000 genomes]
rs13139132	0.90[EUR][1000 genomes]
rs13147381	0.86[EUR][1000 genomes]
rs17086249	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412717	0.86[EUR][1000 genomes]
rs2412718	0.86[EUR][1000 genomes]
rs2412719	0.85[EUR][1000 genomes]
rs2412720	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412721	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412722	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412725	0.88[ASN][1000 genomes]
rs2412726	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412728	0.91[EUR][1000 genomes]
rs2702332	0.90[EUR][1000 genomes]
rs34181414	0.86[EUR][1000 genomes]
rs34546346	0.86[ASN][1000 genomes]
rs34577487	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34683632	0.86[EUR][1000 genomes]
rs34796075	0.84[EUR][1000 genomes]
rs35400594	0.86[EUR][1000 genomes]
rs35417087	0.81[EUR][1000 genomes]
rs35736349	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35770075	0.86[EUR][1000 genomes]
rs35786306	0.86[EUR][1000 genomes]
rs35786805	0.87[EUR][1000 genomes]
rs35976456	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36092812	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4355456	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364320	0.86[EUR][1000 genomes]
rs4645275	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58795379	0.86[EUR][1000 genomes]
rs59053231	0.93[ASN][1000 genomes]
rs59838410	0.86[ASN][1000 genomes]
rs60296378	0.86[ASN][1000 genomes]
rs6554328	0.86[EUR][1000 genomes]
rs6819574	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6826903	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836376	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6839220	0.85[EUR][1000 genomes]
rs6839870	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601617	0.85[EUR][1000 genomes]
rs73155600	0.91[ASN][1000 genomes]
rs73155601	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73162699	0.95[ASN][1000 genomes]
rs73162701	0.89[ASN][1000 genomes]
rs7657181	0.83[EUR][1000 genomes]
rs7659694	0.86[EUR][1000 genomes]
rs7663270	0.84[EUR][1000 genomes]
rs7672541	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676365	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7685766	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56916400-56936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:56916600-56921200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:56916600-56921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:56916600-56921600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:56916600-56929400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:56916600-56931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:56916600-56934200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:56916800-56921400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:56917000-56921200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:56917200-56921200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:56917200-56921200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:56917200-56921200	Weak transcription	Fetal Intestine Large	intestine
13	chr4:56917200-56921200	Weak transcription	HepG2	liver
14	chr4:56917200-56921600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:56917200-56922400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:56917200-56923600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:56917200-56934600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:56917800-56921600	Weak transcription	Fetal Kidney	kidney
19	chr4:56919000-56921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:56919200-56921200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:56919200-56921600	Weak transcription	Fetal Lung	lung
22	chr4:56919400-56921200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:56919400-56921600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:56919600-56921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:56920200-56922000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:56920200-56922200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:56920600-56921200	Enhancers	Brain Germinal Matrix	brain
28	chr4:56920600-56921600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:56920600-56922000	Enhancers	Fetal Brain Male	brain
30	chr4:56921000-56921800	Flanking Active TSS	Fetal Brain Female	brain
31	chr4:56921000-56922000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr4:56921000-56922000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr4:56921000-56922200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:56921000-56922200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr4:56921000-56922200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:56921000-56922400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:56921000-56922400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr4:56921000-56922600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr4:56921000-56922600	Enhancers	Duodenum Mucosa	Duodenum
40	chr4:56921000-56923600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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