Variant report

Variant	rs2016490
Chromosome Location	chr2:54210009-54210010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54196698..54199249-chr2:54209378..54211786,2	MCF-7	breast:
2	chr2:54196641..54201530-chr2:54208327..54212751,6	K562	blood:
3	chr2:54209836..54212670-chr2:54227485..54229972,3	MCF-7	breast:
4	chr2:54197131..54199961-chr2:54207547..54210724,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12052354	0.84[ASN][1000 genomes]
rs17045435	0.80[ASN][1000 genomes]
rs2293359	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2293360	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55940356	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56264825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58879065	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58985250	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
2	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
3	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
7	chr2:54199200-54210600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
9	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
10	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
11	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
12	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
13	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:54199200-54214200	Weak transcription	NH-A	brain
16	chr2:54199200-54214400	Weak transcription	A549	lung
17	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:54200200-54211400	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:54200200-54212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
22	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:54201400-54211400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:54201400-54211400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54201800-54211600	Strong transcription	Primary T cells from cord blood	blood
26	chr2:54202200-54212600	Weak transcription	HepG2	liver
27	chr2:54202600-54211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:54202600-54214200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:54202600-54214400	Weak transcription	NHDF-Ad	bronchial
30	chr2:54202800-54214800	Weak transcription	NHLF	lung
31	chr2:54202800-54215800	Weak transcription	NHEK	skin
32	chr2:54203200-54214200	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:54203600-54214800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:54203800-54210400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:54203800-54211600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:54203800-54214200	Weak transcription	Brain Anterior Caudate	brain
37	chr2:54204000-54210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea
39	chr2:54204600-54214000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:54204600-54214200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:54205000-54213800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:54205200-54222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:54205800-54211400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:54205800-54212400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:54206000-54212800	Weak transcription	Left Ventricle	heart
46	chr2:54206000-54214200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:54206000-54214200	Weak transcription	GM12878-XiMat	blood
48	chr2:54206000-54216600	Weak transcription	Esophagus	oesophagus
49	chr2:54206000-54221600	Weak transcription	Thymus	Thymus
50	chr2:54206000-54226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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