Variant report

Variant	rs28689042
Chromosome Location	chr4:144145396-144145397
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	chr4:144105509..144108491-chr4:144144568..144147316,2	MCF-7	breast:
2	chr4:144144729..144146832-chr4:144161268..144163289,2	K562	blood:

Variant related genes	Relation type
ENSG00000250326	Chromatin interaction
ENSG00000170185	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10003936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10007068	1.00[EUR][1000 genomes]
rs10008314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017771	1.00[EUR][1000 genomes]
rs10021800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022882	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10023498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050163	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931764	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947101	1.00[ASN][1000 genomes]
rs28375333	1.00[EUR][1000 genomes]
rs28412476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431915	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478042	1.00[EUR][1000 genomes]
rs28507672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514400	1.00[EUR][1000 genomes]
rs28562579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655338	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28684892	1.00[EUR][1000 genomes]
rs28704746	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28925889	1.00[ASN][1000 genomes]
rs28989231	1.00[ASN][1000 genomes]
rs300922	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3196542	1.00[EUR][1000 genomes]
rs6822036	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825700	1.00[EUR][1000 genomes]
rs6845309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680827	1.00[ASN][1000 genomes]
rs9992969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996641	1.00[EUR][1000 genomes];1.00[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	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144110200-144145600	Weak transcription	Stomach Mucosa	stomach
2	chr4:144118400-144150000	Weak transcription	Aorta	Aorta
3	chr4:144120600-144147000	Weak transcription	Esophagus	oesophagus
4	chr4:144120800-144149400	Weak transcription	Pancreas	Pancrea
5	chr4:144122400-144145600	Weak transcription	Right Ventricle	heart
6	chr4:144122800-144145800	Weak transcription	Colonic Mucosa	Colon
7	chr4:144125800-144155600	Weak transcription	Fetal Stomach	stomach
8	chr4:144126600-144146200	Weak transcription	A549	lung
9	chr4:144128200-144148600	Weak transcription	K562	blood
10	chr4:144133600-144145400	Weak transcription	NHDF-Ad	bronchial
11	chr4:144135200-144145400	Weak transcription	Gastric	stomach
12	chr4:144135200-144145600	Weak transcription	Small Intestine	intestine
13	chr4:144135200-144146600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:144135200-144151400	Weak transcription	Lung	lung
15	chr4:144135800-144146200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:144135800-144148000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:144135800-144151400	Weak transcription	Left Ventricle	heart
18	chr4:144135800-144153400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:144136000-144145600	Weak transcription	Fetal Intestine Large	intestine
20	chr4:144136000-144145600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:144136000-144148200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:144136000-144148200	Weak transcription	Brain Germinal Matrix	brain
23	chr4:144136000-144148400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:144136000-144149200	Weak transcription	Psoas Muscle	Psoas
25	chr4:144136000-144149600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:144136000-144149600	Weak transcription	Thymus	Thymus
27	chr4:144136200-144148000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:144136200-144148200	Weak transcription	Brain Anterior Caudate	brain
29	chr4:144136400-144146200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:144136400-144147000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:144136400-144148400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:144136400-144151600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:144136600-144145600	Weak transcription	Fetal Lung	lung
34	chr4:144136600-144146400	Weak transcription	Primary B cells from cord blood	blood
35	chr4:144136600-144148000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:144136600-144148400	Weak transcription	Fetal Brain Male	brain
37	chr4:144136800-144145600	Weak transcription	Placenta	Placenta
38	chr4:144137000-144150800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:144137200-144148400	Weak transcription	Fetal Brain Female	brain
40	chr4:144138200-144145600	Weak transcription	Fetal Intestine Small	intestine
41	chr4:144139800-144146800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:144140000-144145800	Weak transcription	Brain Angular Gyrus	brain
43	chr4:144140800-144146800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:144141000-144146000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr4:144142000-144146000	Weak transcription	HUVEC	blood vessel
46	chr4:144142000-144148000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:144142000-144148200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:144142200-144145600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:144142400-144145600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr4:144142800-144146400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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