Variant report

Variant	rs58552166
Chromosome Location	chr2:48112019-48112020
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48101529..48104019-chr2:48110699..48112779,2	K562	blood:
2	chr2:48109295..48112069-chr2:48114485..48118644,4	K562	blood:
3	chr2:48111533..48113899-chr2:48130975..48133874,2	K562	blood:
4	chr2:48111817..48115456-chr2:48131838..48134984,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233230	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10490303	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10495948	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17036952	0.90[AMR][1000 genomes]
rs17036971	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17037021	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037040	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17037055	0.87[EUR][1000 genomes]
rs17037062	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17037064	0.87[EUR][1000 genomes]
rs2134055	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2881863	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136242	0.90[AMR][1000 genomes]
rs3136274	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136286	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4381823	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56682209	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56881113	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58057481	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59624704	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60118201	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60303023	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72876814	0.89[EUR][1000 genomes]
rs7560678	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
6	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523013	chr2:48073117-48146122	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48065400-48114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48067000-48122000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:48089800-48121000	Weak transcription	Aorta	Aorta
4	chr2:48095000-48118200	Weak transcription	NH-A	brain
5	chr2:48095200-48118400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:48095200-48127200	Weak transcription	Fetal Kidney	kidney
7	chr2:48095400-48118200	Weak transcription	HMEC	breast
8	chr2:48095400-48129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:48096000-48123400	Weak transcription	Esophagus	oesophagus
10	chr2:48097800-48123400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:48098000-48118400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:48098000-48122400	Weak transcription	Fetal Brain Male	brain
13	chr2:48098200-48115200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:48098200-48115400	Weak transcription	HSMM	muscle
15	chr2:48098400-48112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:48098400-48117400	Weak transcription	Placenta	Placenta
17	chr2:48098400-48119600	Weak transcription	Liver	Liver
18	chr2:48098400-48125000	Weak transcription	HUVEC	blood vessel
19	chr2:48098600-48117600	Weak transcription	Left Ventricle	heart
20	chr2:48098600-48119200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:48098600-48121000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:48098600-48129000	Weak transcription	Gastric	stomach
23	chr2:48098600-48129000	Weak transcription	Pancreas	Pancrea
24	chr2:48099000-48118200	Weak transcription	NHDF-Ad	bronchial
25	chr2:48099400-48115800	Weak transcription	Fetal Heart	heart
26	chr2:48099600-48118400	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:48099800-48112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:48099800-48115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:48100400-48115600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:48100600-48121000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:48100600-48129200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:48100800-48112400	Weak transcription	Right Atrium	heart
33	chr2:48100800-48120600	Weak transcription	K562	blood
34	chr2:48101000-48112200	Weak transcription	Brain Angular Gyrus	brain
35	chr2:48101000-48115400	Weak transcription	HSMMtube	muscle
36	chr2:48101000-48118600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:48101000-48119600	Weak transcription	Adipose Nuclei	Adipose
38	chr2:48101200-48112400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:48101200-48114000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:48101200-48114600	Weak transcription	Lung	lung
41	chr2:48101200-48114600	Weak transcription	Dnd41	blood
42	chr2:48101200-48117200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:48101200-48119400	Weak transcription	Psoas Muscle	Psoas
44	chr2:48101200-48123600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:48101400-48114200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:48102000-48112400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:48102400-48118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:48103600-48115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:48107400-48114800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:48107400-48115000	Weak transcription	Small Intestine	intestine

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