Variant report

Variant	rs56398518
Chromosome Location	chr3:47500452-47500453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47500348..47503625-chr3:47514780..47518707,3	K562	blood:
2	chr3:47495443..47497442-chr3:47500032..47502167,2	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1038392	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106745	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59825859	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72911242	0.81[AMR][1000 genomes]
rs72911269	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72911287	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7642630	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv1816532	chr3:47490712-47511698	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1841538	chr3:47490712-47511698	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1848062	chr3:47490712-47511698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv1849930	chr3:47490712-47511698	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
4	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:47484600-47500600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:47484800-47504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:47484800-47504600	Weak transcription	Primary T cells from cord blood	blood
14	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
15	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:47485200-47502600	Weak transcription	K562	blood
17	chr3:47485400-47503200	Weak transcription	Gastric	stomach
18	chr3:47486000-47504600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
21	chr3:47486000-47516000	Weak transcription	HSMM	muscle
22	chr3:47486200-47502600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:47486200-47506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:47486600-47500600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:47487000-47502400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:47493400-47510800	Weak transcription	Spleen	Spleen
28	chr3:47494000-47503000	Weak transcription	Right Ventricle	heart
29	chr3:47494200-47500600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:47494400-47504200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:47494400-47506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:47494600-47508200	Weak transcription	Fetal Stomach	stomach
33	chr3:47494600-47514000	Weak transcription	Esophagus	oesophagus
34	chr3:47494600-47514000	Weak transcription	Pancreas	Pancrea
35	chr3:47494800-47504400	Weak transcription	Left Ventricle	heart
36	chr3:47494800-47511200	Weak transcription	Psoas Muscle	Psoas
37	chr3:47495400-47514600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:47497000-47504400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:47497600-47500600	Weak transcription	Brain Anterior Caudate	brain
40	chr3:47497600-47511400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:47497800-47500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:47497800-47500800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:47497800-47502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:47497800-47504400	Weak transcription	Stomach Mucosa	stomach
45	chr3:47497800-47511400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:47497800-47514800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:47497800-47514800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:47497800-47514800	Weak transcription	Hela-S3	cervix
49	chr3:47497800-47516000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:47497800-47516000	Weak transcription	A549	lung

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