Variant report

Variant	rs28612590
Chromosome Location	chr4:95488567-95488568
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95479530..95482092-chr4:95487778..95489313,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10009358	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10011209	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10017461	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10019452	0.92[ASN][1000 genomes]
rs10023909	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10026467	0.80[EUR][1000 genomes]
rs10034254	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10516952	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11722955	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11731783	0.92[ASN][1000 genomes]
rs11735827	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331549	1.00[ASN][1000 genomes]
rs17021775	0.91[EUR][1000 genomes]
rs17021818	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021822	0.96[ASN][1000 genomes]
rs17336470	0.92[ASN][1000 genomes]
rs1812924	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2006927	0.92[ASN][1000 genomes]
rs28492872	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28533860	0.92[ASN][1000 genomes]
rs28560157	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28579984	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28690414	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28717041	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792662	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3792665	0.86[EUR][1000 genomes]
rs3805265	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805282	0.80[EUR][1000 genomes]
rs55858829	0.91[EUR][1000 genomes]
rs62316475	0.92[ASN][1000 genomes]
rs62316476	0.92[ASN][1000 genomes]
rs62316477	0.92[ASN][1000 genomes]
rs6840774	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6841895	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7690869	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9307143	0.86[EUR][1000 genomes]
rs9307145	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9307146	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9994440	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9997947	0.92[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	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:95470000-95489200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:95470600-95489200	Weak transcription	Small Intestine	intestine
4	chr4:95479800-95491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:95479800-95496800	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:95481200-95494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:95481400-95496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:95481400-95496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:95483200-95488800	Weak transcription	K562	blood
10	chr4:95483400-95491600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:95483400-95491800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:95483400-95496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:95483400-95496800	Weak transcription	NHEK	skin
14	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:95483600-95496200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:95483800-95488800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:95483800-95491800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:95483800-95496600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:95483800-95496800	Weak transcription	Gastric	stomach
20	chr4:95483800-95497000	Weak transcription	HMEC	breast
21	chr4:95484000-95488600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:95484000-95488800	Weak transcription	Adipose Nuclei	Adipose
23	chr4:95484000-95488800	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:95484000-95489000	Weak transcription	Stomach Mucosa	stomach
25	chr4:95484000-95491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:95484000-95495600	Weak transcription	NH-A	brain
27	chr4:95484000-95496600	Weak transcription	HSMMtube	muscle
28	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
29	chr4:95484600-95496800	Weak transcription	HSMM	muscle
30	chr4:95484800-95488800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:95485600-95488800	Weak transcription	Right Atrium	heart
32	chr4:95485600-95496600	Weak transcription	Ovary	ovary
33	chr4:95485800-95488600	Weak transcription	Osteobl	bone
34	chr4:95485800-95488800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:95485800-95488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:95485800-95495200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:95485800-95496800	Weak transcription	Psoas Muscle	Psoas
38	chr4:95485800-95496800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:95486000-95489000	Weak transcription	Fetal Intestine Small	intestine
40	chr4:95486000-95496800	Weak transcription	Aorta	Aorta
41	chr4:95486200-95495000	Weak transcription	Placenta	Placenta
42	chr4:95486200-95495200	Weak transcription	Left Ventricle	heart
43	chr4:95486400-95493200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:95486800-95488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:95486800-95490400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:95486800-95496600	Weak transcription	Right Ventricle	heart
47	chr4:95487000-95495200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:95487000-95496600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:95487200-95488800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:95487200-95489400	Enhancers	A549	lung

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