Variant report

Variant	rs1462988
Chromosome Location	chr4:22489538-22489539
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	chr4:22488399..22490950-chr4:22493521..22495053,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10938903	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728370	0.80[CHB][hapmap]
rs13103323	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13113896	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1381915	0.82[CHB][hapmap]
rs1462987	0.82[CHB][hapmap]
rs16872759	0.80[CHB][hapmap]
rs1841823	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4631026	0.82[CHB][hapmap]
rs4697014	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4697015	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4697018	0.91[CHB][hapmap]
rs4697308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4697309	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6818676	0.82[CHB][hapmap]
rs7692390	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap]
rs7697048	0.91[CHB][hapmap];0.81[CHD][hapmap]

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	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv878752	chr4:22414023-22501043	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:22462000-22493200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:22484200-22490400	Enhancers	Fetal Muscle Leg	muscle
4	chr4:22484800-22492400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:22484800-22493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:22484800-22498400	Weak transcription	Gastric	stomach
7	chr4:22485000-22490200	Enhancers	Colon Smooth Muscle	Colon
8	chr4:22485000-22492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:22485000-22506000	Weak transcription	Esophagus	oesophagus
10	chr4:22485400-22492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:22485600-22489600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:22485600-22492400	Weak transcription	Liver	Liver
13	chr4:22485600-22493200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:22485600-22501400	Weak transcription	Hela-S3	cervix
15	chr4:22485600-22502000	Weak transcription	A549	lung
16	chr4:22485800-22491600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr4:22486400-22500600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:22486600-22489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:22486600-22492200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:22486600-22492200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:22486600-22492400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:22486800-22490200	Enhancers	Left Ventricle	heart
23	chr4:22486800-22490200	Enhancers	Psoas Muscle	Psoas
24	chr4:22486800-22492400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:22487000-22489600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:22487200-22490200	Enhancers	Fetal Heart	heart
27	chr4:22487200-22490200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:22487400-22489800	Enhancers	Rectal Smooth Muscle	rectum
29	chr4:22487400-22490200	Enhancers	Right Ventricle	heart
30	chr4:22487800-22489600	Enhancers	HSMM	muscle
31	chr4:22487800-22490600	Enhancers	HepG2	liver
32	chr4:22487800-22492400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:22488000-22489600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:22488000-22489600	Enhancers	Pancreas	Pancrea
35	chr4:22488000-22490200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:22488000-22494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:22488200-22491400	Weak transcription	Aorta	Aorta
38	chr4:22488400-22503000	Weak transcription	Small Intestine	intestine
39	chr4:22488600-22490400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr4:22488600-22516000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:22488800-22489600	Weak transcription	Fetal Kidney	kidney
42	chr4:22488800-22496800	Weak transcription	HMEC	breast
43	chr4:22488800-22497800	Weak transcription	NHEK	skin
44	chr4:22488800-22503600	Weak transcription	NHLF	lung
45	chr4:22489000-22489600	Enhancers	Brain Cingulate Gyrus	brain
46	chr4:22489000-22490200	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:22489000-22490200	Enhancers	Right Atrium	heart
48	chr4:22489000-22490400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:22489000-22490400	Weak transcription	Fetal Intestine Large	intestine
50	chr4:22489200-22489800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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