Variant report

Variant	rs58204287
Chromosome Location	chr2:54827624-54827625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54785770..54787299-chr2:54826149..54827905,2	K562	blood:
2	chr2:54822696..54824811-chr2:54826177..54828033,3	K562	blood:
3	chr2:54815022..54818519-chr2:54825874..54828742,4	K562	blood:
4	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1431973	1.00[AMR][1000 genomes]
rs1431974	1.00[AMR][1000 genomes]
rs3796015	0.83[AFR][1000 genomes]
rs55633042	1.00[AMR][1000 genomes]
rs56196255	1.00[AMR][1000 genomes]
rs56951671	1.00[AMR][1000 genomes]
rs57086836	0.82[AFR][1000 genomes]
rs57406175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57539931	1.00[AMR][1000 genomes]
rs57926982	1.00[AMR][1000 genomes]
rs58924163	1.00[AMR][1000 genomes]
rs58987524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59061110	1.00[AMR][1000 genomes]
rs59402608	1.00[AMR][1000 genomes]
rs60293507	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60542617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60611759	1.00[AMR][1000 genomes]
rs6740921	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73934512	1.00[AMR][1000 genomes]
rs73934514	1.00[AMR][1000 genomes]
rs73934808	1.00[AMR][1000 genomes]
rs73934809	1.00[AMR][1000 genomes]
rs73937514	1.00[AMR][1000 genomes]
rs73938306	1.00[AMR][1000 genomes]
rs7570695	0.92[AFR][1000 genomes];1.00[AMR][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA 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	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:54822200-54833800	Genic enhancers	HepG2	liver
7	chr2:54822400-54827800	Enhancers	Colon Smooth Muscle	Colon
8	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
9	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
10	chr2:54822400-54834000	Enhancers	Right Atrium	heart
11	chr2:54822800-54831600	Genic enhancers	A549	lung
12	chr2:54823200-54831000	Genic enhancers	Fetal Intestine Large	intestine
13	chr2:54823800-54829400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:54824000-54829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:54824200-54829600	Enhancers	Fetal Heart	heart
16	chr2:54824200-54830600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:54824200-54833600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:54824400-54828800	Enhancers	HMEC	breast
19	chr2:54824400-54829200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:54824600-54834400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:54824800-54829600	Genic enhancers	Primary hematopoietic stem cells	blood
22	chr2:54824800-54834400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:54825000-54829200	Genic enhancers	HSMM	muscle
25	chr2:54825000-54829800	Weak transcription	Fetal Brain Male	brain
26	chr2:54825200-54828400	Strong transcription	GM12878-XiMat	blood
27	chr2:54825400-54827800	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr2:54825400-54828200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:54825400-54828800	Strong transcription	Fetal Stomach	stomach
30	chr2:54825400-54829000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:54825600-54827800	Genic enhancers	Brain Anterior Caudate	brain
32	chr2:54825600-54827800	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr2:54825600-54828400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:54825600-54828400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:54825600-54828600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:54825800-54827800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:54825800-54827800	Enhancers	Aorta	Aorta
38	chr2:54825800-54828400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:54825800-54829600	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:54826000-54827800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:54826000-54827800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr2:54826000-54827800	Genic enhancers	Liver	Liver
43	chr2:54826000-54828400	Strong transcription	Primary B cells from cord blood	blood
44	chr2:54826000-54828800	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr2:54826000-54829600	Genic enhancers	Fetal Thymus	thymus
46	chr2:54826000-54831200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:54826200-54827800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:54826200-54827800	Genic enhancers	Left Ventricle	heart
49	chr2:54826200-54828400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr2:54826200-54829000	Genic enhancers	NH-A	brain

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