Variant report

Variant	rs2412405
Chromosome Location	chr4:54013975-54013976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54007557..54010483-chr4:54011201..54014968,3	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13141154	0.86[AFR][1000 genomes]
rs2368380	0.93[AFR][1000 genomes]
rs3849655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3910858	0.89[AFR][1000 genomes]
rs4864447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4864719	0.89[AFR][1000 genomes]
rs6554066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6834711	0.84[AFR][1000 genomes]
rs7659856	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3356275	chr4:54013236-54015318	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53987800-54016800	Weak transcription	NHLF	lung
2	chr4:53993800-54027800	Weak transcription	Fetal Stomach	stomach
3	chr4:53995200-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:53995400-54017800	Weak transcription	Brain Substantia Nigra	brain
5	chr4:53997000-54017600	Weak transcription	Gastric	stomach
6	chr4:53997400-54020000	Weak transcription	HSMM	muscle
7	chr4:53998600-54014400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:53999000-54017200	Weak transcription	Fetal Lung	lung
9	chr4:53999000-54027800	Weak transcription	NHDF-Ad	bronchial
10	chr4:54001200-54017600	Weak transcription	Spleen	Spleen
11	chr4:54003400-54019000	Weak transcription	GM12878-XiMat	blood
12	chr4:54004000-54017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:54004200-54020800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:54005600-54023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:54007000-54017600	Weak transcription	Right Ventricle	heart
17	chr4:54007200-54030600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:54008200-54017200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:54008200-54017600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:54008600-54019000	Weak transcription	Fetal Intestine Small	intestine
21	chr4:54008800-54017400	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:54009200-54017200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:54009400-54016400	Weak transcription	Placenta	Placenta
24	chr4:54009400-54017400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:54009600-54017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:54009600-54017600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:54009600-54017600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:54009600-54024000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:54009800-54017800	Weak transcription	Colonic Mucosa	Colon
30	chr4:54010200-54034600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:54011400-54017600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:54011400-54027800	Weak transcription	Aorta	Aorta
33	chr4:54011600-54016200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:54011600-54017200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:54011600-54017200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:54011600-54017200	Weak transcription	Dnd41	blood
37	chr4:54011600-54017400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:54011600-54017400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:54011600-54017600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:54011600-54017600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:54011600-54019000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:54011600-54019000	Weak transcription	Lung	lung
43	chr4:54011600-54021000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:54011600-54021000	Weak transcription	Primary B cells from cord blood	blood
45	chr4:54011600-54021400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:54011600-54022600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr4:54011600-54027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:54011600-54027800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:54011600-54029200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:54011600-54030600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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