Variant report

Variant	rs62489374
Chromosome Location	chr7:129581482-129581483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129580973..129583222-chr7:129589098..129590720,2	MCF-7	breast:
2	chr7:129580393..129583489-chr7:129591142..129594108,4	MCF-7	breast:
3	chr7:129580130..129583281-chr7:129591250..129593438,3	K562	blood:
4	chr7:129578475..129582652-chr7:129591103..129594701,5	MCF-7	breast:
5	chr7:129580280..129582839-chr7:129588258..129589912,2	MCF-7	breast:
6	chr7:129573624..129576987-chr7:129579188..129581897,3	K562	blood:
7	chr7:129536776..129538391-chr7:129580195..129581727,2	K562	blood:

Variant related genes	Relation type
ENSG00000186591	Chromatin interaction
ENSG00000244036	Chromatin interaction
ENSG00000199516	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10215972	0.83[AFR][1000 genomes]
rs10216153	0.84[AFR][1000 genomes]
rs10216157	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10240142	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10242002	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246707	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249037	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253233	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261367	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273782	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046691	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500121	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486831	0.83[AFR][1000 genomes]
rs1526323	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162050	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162123	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162136	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162295	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639187	1.00[ASN][1000 genomes]
rs2037720	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28604351	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297290	0.83[AFR][1000 genomes]
rs55682483	0.83[AFR][1000 genomes]
rs57314877	0.83[AFR][1000 genomes]
rs58857902	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62489375	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491492	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491503	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491504	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62491537	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467267	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962745	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6979056	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161641	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783328	0.87[AFR][1000 genomes]
rs7789191	0.90[AFR][1000 genomes]
rs7789336	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801603	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803795	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656386	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv831129	chr7:129525406-129702477	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129516200-129584400	Weak transcription	Fetal Brain Male	brain
2	chr7:129530000-129587600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:129549200-129586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:129549800-129588200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:129555200-129587000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:129556600-129588000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:129557400-129587000	Weak transcription	Fetal Lung	lung
8	chr7:129558000-129584600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:129558000-129587600	Weak transcription	Brain Germinal Matrix	brain
10	chr7:129559600-129588000	Weak transcription	Esophagus	oesophagus
11	chr7:129559800-129588600	Weak transcription	Colonic Mucosa	Colon
12	chr7:129564400-129586800	Weak transcription	A549	lung
13	chr7:129565200-129587400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:129565400-129587400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:129565600-129586400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:129565600-129587600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:129565600-129588200	Weak transcription	HMEC	breast
18	chr7:129565800-129584400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:129565800-129586600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:129565800-129586800	Weak transcription	Brain Anterior Caudate	brain
21	chr7:129565800-129587000	Weak transcription	NH-A	brain
22	chr7:129565800-129587400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:129565800-129587600	Weak transcription	Brain Angular Gyrus	brain
24	chr7:129565800-129588200	Weak transcription	HUVEC	blood vessel
25	chr7:129566000-129584400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:129566000-129586400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:129566000-129586400	Weak transcription	NHDF-Ad	bronchial
28	chr7:129566000-129587000	Weak transcription	Adipose Nuclei	Adipose
29	chr7:129566000-129587000	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:129566200-129586800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:129568200-129584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:129569000-129588000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:129569400-129584400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:129569600-129586400	Weak transcription	Liver	Liver
35	chr7:129569800-129587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:129570000-129583000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:129570000-129584400	Weak transcription	Fetal Brain Female	brain
38	chr7:129570000-129585800	Weak transcription	Placenta	Placenta
39	chr7:129570200-129587400	Weak transcription	Stomach Mucosa	stomach
40	chr7:129570400-129581800	Weak transcription	Primary T cells from cord blood	blood
41	chr7:129571000-129586200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:129573200-129588200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:129573400-129586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:129573400-129586800	Weak transcription	NHLF	lung
45	chr7:129573400-129587400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:129573600-129582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:129573600-129586200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:129573800-129583000	Weak transcription	Primary B cells from cord blood	blood
49	chr7:129573800-129583200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:129573800-129586400	Weak transcription	Hela-S3	cervix

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