Variant report

Variant	rs28406334
Chromosome Location	chr2:40004938-40004939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39956738..39958463-chr2:40003948..40005760,2	K562	blood:
2	chr2:39961424..39963272-chr2:40004019..40005990,2	K562	blood:
3	chr2:39739040..39741917-chr2:40004865..40006467,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10177342	0.90[AFR][1000 genomes]
rs12712654	0.84[AFR][1000 genomes]
rs12712655	0.84[AFR][1000 genomes]
rs13393172	0.84[AFR][1000 genomes]
rs13412186	0.86[AFR][1000 genomes]
rs57728145	0.93[AFR][1000 genomes]
rs59146573	0.85[AFR][1000 genomes]
rs59943821	0.85[AMR][1000 genomes]
rs6544243	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6744797	0.98[AFR][1000 genomes]
rs6749057	0.81[AFR][1000 genomes]
rs7564579	0.86[AFR][1000 genomes]

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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
4	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
6	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:39985800-40005400	Weak transcription	Lung	lung
9	chr2:39996400-40005000	Weak transcription	Stomach Mucosa	stomach
10	chr2:39997000-40005200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr2:39997000-40005400	Weak transcription	Placenta	Placenta
12	chr2:39997000-40005800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:39999000-40005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:39999600-40005200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:40000000-40006000	Weak transcription	Spleen	Spleen
16	chr2:40000200-40005000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:40000200-40005000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:40000200-40005000	Weak transcription	Brain Substantia Nigra	brain
19	chr2:40000200-40006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:40001000-40005200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:40001000-40006600	Active TSS	GM12878-XiMat	blood
22	chr2:40001400-40005000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:40001400-40005000	Weak transcription	Right Atrium	heart
24	chr2:40001400-40005000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:40001400-40005400	Weak transcription	Gastric	stomach
26	chr2:40001400-40005400	Weak transcription	Left Ventricle	heart
27	chr2:40002400-40005000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:40002800-40005000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:40002800-40005400	Weak transcription	Esophagus	oesophagus
30	chr2:40002800-40005400	Weak transcription	Pancreas	Pancrea
31	chr2:40003000-40005200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:40003400-40005200	Transcr. at gene 5' and 3'	K562	blood
33	chr2:40003600-40005000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:40003600-40005400	Flanking Active TSS	Dnd41	blood
35	chr2:40003800-40005800	Enhancers	Small Intestine	intestine
36	chr2:40004000-40005000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr2:40004000-40006000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:40004200-40005000	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:40004200-40005000	Weak transcription	HSMM	muscle
40	chr2:40004200-40005200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:40004200-40005200	Enhancers	Fetal Heart	heart
42	chr2:40004200-40005400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:40004200-40005400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:40004200-40006600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:40004200-40006600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:40004200-40006600	Active TSS	HSMMtube	muscle
47	chr2:40004200-40008800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:40004400-40005000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:40004400-40005000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:40004400-40005200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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