Variant report

Variant	rs28394039
Chromosome Location	chr4:106169923-106169924
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	chr4:106074483..106076785-chr4:106168679..106171632,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10003144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006632	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006721	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008189	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017522	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018267	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022126	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023701	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10026237	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027791	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033325	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932794	0.97[ASN][1000 genomes]
rs11938493	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941838	1.00[ASN][1000 genomes]
rs11943394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944001	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944085	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947617	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505746	0.89[ASN][1000 genomes]
rs2017763	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655620	0.82[ASN][1000 genomes]
rs28707121	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796927	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235413	0.92[ASN][1000 genomes]
rs55793049	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58862751	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59339947	0.95[ASN][1000 genomes]
rs59806714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60886348	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826102	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831247	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831445	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833560	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6835030	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843141	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6857812	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955198	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73836047	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836048	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836052	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836055	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73838074	1.00[ASN][1000 genomes]
rs7662448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696287	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696337	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698398	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698522	0.92[ASN][1000 genomes]
rs7700148	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871215	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931653	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9985622	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9993497	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9998069	1.00[EUR][1000 genomes];1.00[ASN][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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:106142000-106190800	Weak transcription	Small Intestine	intestine
4	chr4:106148000-106192800	Weak transcription	Psoas Muscle	Psoas
5	chr4:106150200-106191400	Weak transcription	HUVEC	blood vessel
6	chr4:106154000-106198800	Weak transcription	Hela-S3	cervix
7	chr4:106155000-106176600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:106156600-106180800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:106156800-106190800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:106156800-106196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:106157000-106186000	Weak transcription	NH-A	brain
12	chr4:106157000-106190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:106157400-106193600	Weak transcription	Colonic Mucosa	Colon
14	chr4:106157800-106190600	Weak transcription	NHLF	lung
15	chr4:106158000-106180800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:106158200-106171600	Weak transcription	Fetal Stomach	stomach
17	chr4:106158200-106171800	Weak transcription	Esophagus	oesophagus
18	chr4:106158200-106173000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:106158200-106186600	Weak transcription	Stomach Mucosa	stomach
20	chr4:106158200-106190600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:106158200-106190600	Weak transcription	NHEK	skin
22	chr4:106158200-106190800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:106158200-106190800	Weak transcription	Pancreas	Pancrea
24	chr4:106158200-106190800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:106158200-106190800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:106158400-106171600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:106158400-106173200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:106158400-106190000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:106158400-106190800	Weak transcription	Gastric	stomach
30	chr4:106158400-106190800	Weak transcription	Lung	lung
31	chr4:106159800-106174200	Weak transcription	Fetal Kidney	kidney
32	chr4:106160200-106183200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:106160400-106175400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr4:106161400-106171600	Weak transcription	Left Ventricle	heart
35	chr4:106161400-106172200	Weak transcription	Liver	Liver
36	chr4:106161800-106171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:106162800-106190800	Weak transcription	Fetal Heart	heart
38	chr4:106163400-106174800	Weak transcription	Brain Substantia Nigra	brain
39	chr4:106163400-106196400	Weak transcription	Brain Angular Gyrus	brain
40	chr4:106163600-106190800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:106165000-106182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:106165000-106189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:106165200-106170600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:106165200-106171800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:106165200-106172200	Weak transcription	Primary T cells from cord blood	blood
46	chr4:106165200-106174200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:106165200-106175400	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:106165200-106175600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:106165200-106176400	Weak transcription	Adipose Nuclei	Adipose
50	chr4:106165200-106177600	Weak transcription	Brain Hippocampus Middle	brain

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