Variant report

Variant	rs28855127
Chromosome Location	chr5:52867482-52867483
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	chr5:52858854..52861653-chr5:52864359..52868454,4	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]
rs10513019	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11738542	0.82[AFR][1000 genomes]
rs11740228	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11740800	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11741008	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11743262	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11749849	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16881514	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16881524	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16881561	0.84[ASN][1000 genomes]
rs3958630	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4147735	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147739	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4147742	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4147744	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4549481	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4618398	0.80[ASN][1000 genomes]
rs4640749	0.83[ASN][1000 genomes]
rs6872395	0.80[ASN][1000 genomes]
rs6892641	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72750138	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72750151	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72751832	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72751833	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72751838	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72751849	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72753647	0.84[ASN][1000 genomes]
rs72753650	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72753658	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72757372	0.80[AFR][1000 genomes]
rs7716949	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7729894	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52857200-52872800	Weak transcription	Gastric	stomach
2	chr5:52857200-52872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:52857600-52875000	Weak transcription	Thymus	Thymus
4	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
5	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
7	chr5:52857800-52898800	Weak transcription	HSMM	muscle
8	chr5:52858000-52868800	Weak transcription	Psoas Muscle	Psoas
9	chr5:52858000-52870800	Weak transcription	Primary T cells from cord blood	blood
10	chr5:52858000-52870800	Weak transcription	Ovary	ovary
11	chr5:52858000-52870800	Weak transcription	Right Ventricle	heart
12	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
14	chr5:52858200-52867600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:52858200-52880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:52858200-52897200	Weak transcription	NHEK	skin
18	chr5:52858400-52870800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:52859600-52867600	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:52860000-52870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
24	chr5:52860200-52867600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:52860200-52885600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:52860600-52868800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:52860600-52884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:52861600-52873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:52861600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:52863000-52870600	Weak transcription	Left Ventricle	heart
31	chr5:52865000-52872800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:52865000-52900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:52865200-52868000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:52865200-52885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:52865600-52870800	Weak transcription	HepG2	liver
36	chr5:52865600-52871600	Weak transcription	Liver	Liver
37	chr5:52865600-52871800	Weak transcription	A549	lung
38	chr5:52865600-52872400	Weak transcription	Stomach Mucosa	stomach
39	chr5:52865600-52883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:52865600-52898400	Weak transcription	Fetal Lung	lung
41	chr5:52865600-52899800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:52866200-52883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:52866400-52884200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:52867000-52867600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr5:52867000-52867800	Enhancers	Brain Angular Gyrus	brain
46	chr5:52867000-52867800	Enhancers	Fetal Heart	heart
47	chr5:52867000-52868200	Enhancers	Rectal Smooth Muscle	rectum
48	chr5:52867200-52867600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr5:52867200-52867600	Enhancers	Brain Substantia Nigra	brain
50	chr5:52867200-52867800	Enhancers	Colon Smooth Muscle	Colon

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