Variant report

Variant	rs999139
Chromosome Location	chr15:59496384-59496385
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	chr15:59495521..59497501-chr15:59498771..59500558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157483	Chromatin interaction
ENSG00000171989	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1032180	0.82[EUR][1000 genomes]
rs1032182	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851644	0.84[ASN][1000 genomes]
rs11071413	0.81[ASN][1000 genomes]
rs11634752	0.82[ASN][1000 genomes]
rs11638935	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12898305	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915115	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1565018	0.82[ASN][1000 genomes]
rs2129426	0.84[EUR][1000 genomes]
rs2414623	0.83[ASN][1000 genomes]
rs34412930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764192	0.84[ASN][1000 genomes]
rs3809530	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825937	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162863	0.83[EUR][1000 genomes]
rs7169859	0.83[ASN][1000 genomes]
rs7170182	0.83[ASN][1000 genomes]
rs7178908	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7182279	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs999140	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
3	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
4	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr15:59475200-59503200	Strong transcription	Liver	Liver
6	chr15:59475800-59498200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:59477000-59498000	Strong transcription	GM12878-XiMat	blood
9	chr15:59480200-59499200	Weak transcription	Fetal Lung	lung
10	chr15:59480200-59507200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:59480600-59496400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:59480600-59507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:59482800-59499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:59483200-59514000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:59484200-59499400	Weak transcription	Fetal Kidney	kidney
16	chr15:59485400-59515400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:59485600-59505800	Weak transcription	Brain Germinal Matrix	brain
18	chr15:59485600-59521200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:59487200-59502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:59487600-59498000	Weak transcription	Right Ventricle	heart
21	chr15:59487600-59499400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:59487800-59496400	Weak transcription	Psoas Muscle	Psoas
23	chr15:59487800-59498000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:59487800-59524400	Weak transcription	Small Intestine	intestine
25	chr15:59489600-59503800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:59489800-59501200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:59489800-59512600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:59489800-59515600	Weak transcription	Right Atrium	heart
29	chr15:59490000-59501200	Strong transcription	Fetal Muscle Leg	muscle
30	chr15:59490000-59501200	Strong transcription	Fetal Stomach	stomach
31	chr15:59490200-59502600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:59490200-59510800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:59490600-59501200	Strong transcription	Ovary	ovary
34	chr15:59491000-59498600	Weak transcription	Esophagus	oesophagus
35	chr15:59491400-59501200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:59491400-59501200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:59491600-59503000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr15:59491800-59498400	Strong transcription	Primary B cells from cord blood	blood
39	chr15:59492000-59499000	Strong transcription	Lung	lung
40	chr15:59492000-59501200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:59492000-59503600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:59492000-59521600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr15:59492400-59501200	Strong transcription	Gastric	stomach
44	chr15:59492400-59502400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:59492800-59496600	Weak transcription	Colon Smooth Muscle	Colon
46	chr15:59492800-59499400	Weak transcription	Fetal Heart	heart
47	chr15:59492800-59501200	Strong transcription	Left Ventricle	heart
48	chr15:59493000-59499800	Strong transcription	HSMMtube	muscle
49	chr15:59493000-59501200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:59493000-59501800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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