Variant report

Variant	rs41533648
Chromosome Location	chr2:46933215-46933216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46929305..46931756-chr2:46933052..46934727,2	MCF-7	breast:
2	chr2:46925096..46927639-chr2:46929889..46935400,5	MCF-7	breast:
3	chr2:46933207..46934969-chr2:46956262..46957915,2	K562	blood:
4	chr2:46924668..46928828-chr2:46932943..46938478,8	MCF-7	breast:
5	chr2:46930029..46933528-chr2:46976256..46980348,3	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs41444751	1.00[AMR][1000 genomes]
rs41468249	1.00[AMR][1000 genomes]
rs41481545	1.00[AMR][1000 genomes]
rs59115499	1.00[AMR][1000 genomes]
rs60426444	1.00[AMR][1000 genomes]
rs6715737	1.00[AMR][1000 genomes]
rs72881382	1.00[AMR][1000 genomes]
rs72881388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72881392	1.00[AMR][1000 genomes]
rs72881398	1.00[AMR][1000 genomes]
rs72882805	1.00[AMR][1000 genomes]
rs72882817	1.00[AMR][1000 genomes]
rs72882819	1.00[AMR][1000 genomes]
rs72882829	1.00[AMR][1000 genomes]
rs7598569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46927200-46935800	Weak transcription	Spleen	Spleen
2	chr2:46927400-46933400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:46927400-46933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
6	chr2:46928600-46933600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:46928600-46933600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:46928600-46934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:46928800-46933400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:46928800-46933800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:46928800-46934400	Enhancers	NH-A	brain
13	chr2:46928800-46938600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:46928800-46946200	Weak transcription	NHEK	skin
15	chr2:46929000-46940200	Weak transcription	Fetal Stomach	stomach
16	chr2:46929200-46934400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:46929400-46933400	Weak transcription	Hela-S3	cervix
18	chr2:46929400-46933400	Weak transcription	HMEC	breast
19	chr2:46929400-46933600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:46929600-46934600	Enhancers	Colon Smooth Muscle	Colon
21	chr2:46930000-46934000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:46930000-46934600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:46930000-46934600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:46930000-46938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:46930200-46934400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:46930400-46933400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr2:46930400-46936400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:46931200-46934200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:46931200-46938800	Weak transcription	Primary B cells from cord blood	blood
30	chr2:46931400-46934000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:46931400-46935600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr2:46931600-46933600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:46931600-46934400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr2:46931600-46934600	Enhancers	Liver	Liver
35	chr2:46931600-46935000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr2:46931800-46933800	Enhancers	Small Intestine	intestine
37	chr2:46931800-46934400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:46931800-46936800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:46932000-46933600	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:46932000-46933800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:46932000-46934400	Enhancers	Ovary	ovary
42	chr2:46932000-46935400	Enhancers	Rectal Smooth Muscle	rectum
43	chr2:46932000-46936000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:46932000-46936200	Weak transcription	GM12878-XiMat	blood
45	chr2:46932000-46936400	Enhancers	Adipose Nuclei	Adipose
46	chr2:46932200-46933600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:46932200-46934400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr2:46932200-46934600	Enhancers	HSMM	muscle
49	chr2:46932400-46934000	Flanking Active TSS	Osteobl	bone
50	chr2:46932400-46934400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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