Variant report

Variant	rs16963578
Chromosome Location	chr15:50577964-50577965
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50571295..50573619-chr15:50576803..50579324,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10083714	0.82[ASN][1000 genomes]
rs10152574	0.92[ASN][1000 genomes]
rs11491094	0.82[ASN][1000 genomes]
rs16963562	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs16963571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963573	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs1896169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1955101	0.90[AFR][1000 genomes]
rs28671234	0.86[AMR][1000 genomes]
rs55697237	0.92[ASN][1000 genomes]
rs55774471	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55950921	0.92[ASN][1000 genomes]
rs56812974	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58903525	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59847008	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893904	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs717025	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7177488	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012326	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012336	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012366	0.92[ASN][1000 genomes]
rs74012367	0.92[ASN][1000 genomes]
rs8028745	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8029259	0.82[ASN][1000 genomes]
rs8029439	0.82[ASN][1000 genomes]
rs8034492	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8040420	0.86[ASN][1000 genomes]
rs8040483	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs953159	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9652452	0.82[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50566000-50580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:50567200-50579600	Weak transcription	Fetal Brain Female	brain
4	chr15:50567200-50579600	Weak transcription	Left Ventricle	heart
5	chr15:50567200-50579600	Weak transcription	Ovary	ovary
6	chr15:50567200-50580000	Weak transcription	Brain Germinal Matrix	brain
7	chr15:50567400-50579600	Weak transcription	Thymus	Thymus
8	chr15:50567600-50579600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:50567600-50579600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
11	chr15:50567800-50579800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:50568200-50579600	Weak transcription	Osteobl	bone
14	chr15:50568200-50592000	Weak transcription	NHLF	lung
15	chr15:50568600-50579600	Weak transcription	Fetal Intestine Large	intestine
16	chr15:50568600-50580000	Weak transcription	Esophagus	oesophagus
17	chr15:50568800-50582000	Weak transcription	Stomach Mucosa	stomach
18	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:50569000-50578600	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:50569000-50579600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:50569200-50579600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:50569200-50579600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:50569200-50591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:50569200-50592200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:50569800-50585400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:50570000-50591800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:50570200-50579600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:50570200-50591800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:50570400-50579600	Weak transcription	Lung	lung
32	chr15:50570400-50580200	Weak transcription	Gastric	stomach
33	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:50570800-50579600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:50570800-50579600	Weak transcription	Fetal Intestine Small	intestine
36	chr15:50570800-50591800	Weak transcription	HSMMtube	muscle
37	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
38	chr15:50571000-50592000	Weak transcription	Right Ventricle	heart
39	chr15:50571200-50579600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:50571200-50580000	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:50571200-50593000	Weak transcription	Fetal Kidney	kidney
42	chr15:50572000-50589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:50572400-50579400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:50572600-50579400	Weak transcription	Primary T cells from cord blood	blood
45	chr15:50572800-50579600	Weak transcription	Aorta	Aorta
46	chr15:50572800-50579800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:50572800-50593200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:50573000-50579600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:50573000-50580600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:50573000-50592000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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