Variant report

Variant	rs55728465
Chromosome Location	chr2:112666096-112666097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112661966..112663784-chr2:112664402..112668522,3	K562	blood:
2	chr2:112664770..112667261-chr2:112813197..112815553,2	K562	blood:
3	chr2:112665558..112667722-chr2:112810644..112812668,2	K562	blood:
4	chr2:112661215..112662766-chr2:112664404..112666114,2	MCF-7	breast:
5	chr2:112661967..112663784-chr2:112664402..112666551,2	K562	blood:

Variant related genes	Relation type
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1113419	0.89[EUR][1000 genomes]
rs11884641	0.83[EUR][1000 genomes]
rs11884693	0.83[EUR][1000 genomes]
rs11887652	0.83[EUR][1000 genomes]
rs11893308	0.81[EUR][1000 genomes]
rs11902247	0.89[EUR][1000 genomes]
rs12466812	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469210	0.83[EUR][1000 genomes]
rs12470338	0.89[EUR][1000 genomes]
rs12477716	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400321	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400324	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1400325	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1516629	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17174870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17175275	0.89[EUR][1000 genomes]
rs17175331	0.89[EUR][1000 genomes]
rs17835605	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001201	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2001444	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4278932	0.83[EUR][1000 genomes]
rs4349353	0.83[EUR][1000 genomes]
rs4434006	0.88[EUR][1000 genomes]
rs4521048	0.82[EUR][1000 genomes]
rs4528767	0.82[EUR][1000 genomes]
rs55708724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766181	0.83[EUR][1000 genomes]
rs55785997	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55792453	0.81[EUR][1000 genomes]
rs55799805	0.83[EUR][1000 genomes]
rs55972521	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56272510	0.89[EUR][1000 genomes]
rs57640566	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57732600	0.82[EUR][1000 genomes]
rs58065683	0.83[EUR][1000 genomes]
rs58641606	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59650987	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61583444	0.82[EUR][1000 genomes]
rs6710733	0.82[EUR][1000 genomes]
rs6712080	0.81[EUR][1000 genomes]
rs6729037	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737989	0.81[EUR][1000 genomes]
rs7563113	0.83[EUR][1000 genomes]
rs7568632	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7575552	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578057	0.89[EUR][1000 genomes]
rs867311	0.97[EUR][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	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv998028	chr2:112649472-112734015	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv582701	chr2:112649472-112740597	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv526647	chr2:112651316-112738562	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv582702	chr2:112651316-112738562	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112660200-112674400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:112661600-112666400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:112662800-112667400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:112662800-112675800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:112662800-112677000	Weak transcription	Spleen	Spleen
6	chr2:112663000-112677800	Weak transcription	Right Ventricle	heart
7	chr2:112663600-112667600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:112663800-112668400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:112664200-112667600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:112664200-112667600	Enhancers	Brain Anterior Caudate	brain
11	chr2:112664200-112667600	Enhancers	Fetal Kidney	kidney
12	chr2:112664200-112669000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:112664200-112669000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:112664400-112666400	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:112664400-112666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:112664400-112666800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:112664600-112668200	Weak transcription	Fetal Lung	lung
18	chr2:112664600-112668400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:112664600-112668400	Weak transcription	Small Intestine	intestine
20	chr2:112664600-112668400	Weak transcription	Stomach Mucosa	stomach
21	chr2:112664600-112674400	Weak transcription	Fetal Stomach	stomach
22	chr2:112664600-112675800	Weak transcription	HUVEC	blood vessel
23	chr2:112664600-112676000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:112664600-112676600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:112664600-112687600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:112664600-112702200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:112664800-112666200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:112664800-112666200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:112664800-112667600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:112664800-112668200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:112664800-112668400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:112664800-112668400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:112664800-112668400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:112664800-112670200	Weak transcription	Placenta	Placenta
35	chr2:112664800-112670200	Weak transcription	Right Atrium	heart
36	chr2:112664800-112674600	Weak transcription	Lung	lung
37	chr2:112664800-112675600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:112664800-112676200	Weak transcription	Thymus	Thymus
39	chr2:112664800-112676600	Weak transcription	Pancreas	Pancrea
40	chr2:112665200-112667200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:112665200-112667400	Enhancers	Colon Smooth Muscle	Colon
42	chr2:112665400-112666600	Enhancers	Brain Substantia Nigra	brain
43	chr2:112665400-112666800	Enhancers	K562	blood
44	chr2:112665400-112667800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:112665400-112668400	Enhancers	Liver	Liver
46	chr2:112665600-112666200	Enhancers	Brain Hippocampus Middle	brain
47	chr2:112665600-112666400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:112665600-112666400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:112665600-112666600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:112665600-112667200	Enhancers	HUES64 Cell Line	embryonic stem cell

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