Variant report

Variant	rs41390544
Chromosome Location	chr2:46958392-46958393
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	chr2:46953820..46955350-chr2:46958244..46960079,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1446496	0.85[AFR][1000 genomes]
rs41329944	0.95[AFR][1000 genomes]
rs41449044	0.95[AFR][1000 genomes]
rs41449746	0.95[AFR][1000 genomes]
rs6708132	0.90[AFR][1000 genomes]
rs6712025	0.85[AFR][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	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
7	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 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	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46947600-46975600	Weak transcription	HSMM	muscle
3	chr2:46948200-46962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:46948200-46964400	Weak transcription	NHEK	skin
5	chr2:46948200-46967400	Weak transcription	Esophagus	oesophagus
6	chr2:46948200-46974600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
8	chr2:46948400-46961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:46948600-46964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46948600-46964400	Weak transcription	NH-A	brain
11	chr2:46948600-46974400	Weak transcription	Fetal Stomach	stomach
12	chr2:46949600-46958400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:46950800-46975400	Weak transcription	Fetal Lung	lung
14	chr2:46951400-46962200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:46951800-46959000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:46952000-46961800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:46952600-46962000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:46953400-46964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:46955000-46975400	Weak transcription	Small Intestine	intestine
20	chr2:46955200-46958600	Weak transcription	Primary T cells from cord blood	blood
21	chr2:46955200-46958600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:46955200-46958600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:46955200-46959400	Weak transcription	HepG2	liver
24	chr2:46955200-46961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:46955200-46964600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:46955200-46967600	Weak transcription	Thymus	Thymus
27	chr2:46955200-46970400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:46955200-46974400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:46955200-46984800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:46955200-46985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:46955400-46958400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:46955400-46959400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:46955400-46962000	Weak transcription	Liver	Liver
34	chr2:46955400-46962000	Weak transcription	Pancreas	Pancrea
35	chr2:46955400-46962000	Weak transcription	Psoas Muscle	Psoas
36	chr2:46955400-46962000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:46955400-46967600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:46955400-46967800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:46955400-46967800	Weak transcription	Fetal Thymus	thymus
40	chr2:46955400-46974200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:46955600-46959000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:46955600-46959000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:46955600-46959400	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:46956000-46959000	Weak transcription	Ovary	ovary
45	chr2:46956000-46964200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:46956000-46975400	Weak transcription	Lung	lung
47	chr2:46956000-46980000	Weak transcription	Right Atrium	heart
48	chr2:46956200-46959000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:46956200-46959000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:46956200-46959400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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