Variant report

Variant	rs3754556
Chromosome Location	chr2:46595490-46595491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46593545..46595636-chr2:46687242..46688788,2	MCF-7	breast:
2	chr2:46538986..46541753-chr2:46593488..46595941,2	K562	blood:
3	chr2:46589429..46592507-chr2:46593401..46595603,3	K562	blood:
4	chr2:46582693..46584854-chr2:46594130..46596371,2	K562	blood:
5	chr2:46583354..46585479-chr2:46594871..46597151,2	K562	blood:

Variant related genes	Relation type
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11690950	0.80[CEU][hapmap]
rs12986653	0.82[YRI][hapmap]
rs13002880	0.82[YRI][hapmap]
rs13007688	0.82[YRI][hapmap]
rs13011481	0.82[YRI][hapmap]
rs13019268	0.91[ASW][hapmap]
rs13030579	0.82[YRI][hapmap]
rs1374749	1.00[JPT][hapmap]
rs1530621	0.82[YRI][hapmap]
rs1530633	0.85[YRI][hapmap]
rs1562452	0.85[YRI][hapmap]
rs2121698	0.82[YRI][hapmap]
rs2346176	0.87[MKK][hapmap];0.85[YRI][hapmap]
rs3088359	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs3768730	0.82[YRI][hapmap]
rs4953372	0.82[YRI][hapmap]
rs4953387	0.82[YRI][hapmap]
rs4953388	0.82[YRI][hapmap]
rs4953390	0.82[YRI][hapmap]
rs7594912	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46568000-46596600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
3	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:46574800-46613000	Weak transcription	HSMM	muscle
5	chr2:46580600-46597200	Weak transcription	Fetal Heart	heart
6	chr2:46581200-46597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
8	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
9	chr2:46588800-46596800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:46588800-46597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:46588800-46598800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:46589200-46596200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:46589200-46597000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:46589400-46596200	Weak transcription	Fetal Intestine Large	intestine
15	chr2:46589400-46596800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:46589600-46597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:46589800-46597000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
19	chr2:46590200-46596400	Weak transcription	Esophagus	oesophagus
20	chr2:46590400-46596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:46591000-46596200	Weak transcription	Ovary	ovary
22	chr2:46591000-46596400	Weak transcription	Gastric	stomach
23	chr2:46591000-46596800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:46591200-46596200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46591200-46606400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:46591400-46596600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:46591800-46599800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:46592000-46605000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr2:46592200-46595800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:46592200-46597000	Weak transcription	NHDF-Ad	bronchial
31	chr2:46592200-46619800	Weak transcription	K562	blood
32	chr2:46592600-46598600	Strong transcription	HepG2	liver
33	chr2:46592600-46606600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr2:46592600-46608400	Strong transcription	Osteobl	bone
35	chr2:46592600-46611200	Weak transcription	Primary T cells from cord blood	blood
36	chr2:46592600-46612600	Strong transcription	NHEK	skin
37	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr2:46593000-46595800	Enhancers	Brain Substantia Nigra	brain
39	chr2:46593000-46602600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:46593000-46604000	Strong transcription	Adipose Nuclei	Adipose
41	chr2:46593200-46597600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:46593200-46599600	Genic enhancers	Placenta	Placenta
43	chr2:46593600-46601600	Strong transcription	A549	lung
44	chr2:46593600-46615400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:46594000-46596400	Weak transcription	Fetal Lung	lung
46	chr2:46594000-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:46594200-46604400	Strong transcription	NHLF	lung
48	chr2:46594400-46596800	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:46594400-46599000	Strong transcription	Fetal Intestine Small	intestine
50	chr2:46594400-46615600	Strong transcription	Duodenum Mucosa	Duodenum

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