Variant report

Variant	rs28816429
Chromosome Location	chr5:127302047-127302048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127212523..127214164-chr5:127301948..127304809,2	MCF-7	breast:
2	chr5:127261908..127263560-chr5:127300086..127302066,2	MCF-7	breast:
3	chr5:127301710..127304376-chr5:127421505..127423068,2	MCF-7	breast:
4	chr5:127298909..127302404-chr5:127418523..127420285,3	MCF-7	breast:
5	chr5:127293170..127295868-chr5:127299899..127303794,5	MCF-7	breast:
6	chr5:127256203..127258500-chr5:127301825..127304365,2	MCF-7	breast:
7	chr5:127297981..127299833-chr5:127300238..127305210,4	MCF-7	breast:
8	chr5:127296445..127298165-chr5:127301266..127303118,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC12A2-3	chr5:127301573-127302616	NONHSAT103639

No data

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10037914	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10065448	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10074995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079317	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463834	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10900794	0.92[ASN][1000 genomes]
rs11740438	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740439	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741283	0.92[ASN][1000 genomes]
rs12517005	0.92[ASN][1000 genomes]
rs12653621	0.84[ASN][1000 genomes]
rs12658023	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13361741	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286386	0.82[ASN][1000 genomes]
rs2409037	0.92[ASN][1000 genomes]
rs28473744	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542972	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567046	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28591675	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28636438	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687461	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28736542	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55896045	0.92[ASN][1000 genomes]
rs6877403	0.92[ASN][1000 genomes]
rs6898956	0.92[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
3	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
4	chr5:127293200-127303600	Weak transcription	Esophagus	oesophagus
5	chr5:127294400-127302800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:127295600-127302600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:127295600-127304400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:127295800-127322800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:127296200-127303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:127296200-127303800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:127296200-127304800	Weak transcription	Brain Substantia Nigra	brain
12	chr5:127296200-127306000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:127296200-127307200	Weak transcription	NHLF	lung
14	chr5:127296200-127322600	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:127296400-127302800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:127296400-127302800	Weak transcription	Colonic Mucosa	Colon
17	chr5:127296400-127302800	Weak transcription	HMEC	breast
18	chr5:127296400-127302800	Weak transcription	NHEK	skin
19	chr5:127296400-127303000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:127296400-127303800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:127296400-127304000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:127296400-127304200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:127296400-127304800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:127296400-127304800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:127296400-127305200	Weak transcription	Brain Anterior Caudate	brain
26	chr5:127296400-127306400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:127297000-127305200	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:127297600-127302800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:127297600-127303000	Weak transcription	Thymus	Thymus
30	chr5:127297600-127304600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:127297600-127313200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:127297600-127332000	Weak transcription	Primary B cells from cord blood	blood
33	chr5:127297800-127304000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:127297800-127306400	Weak transcription	Psoas Muscle	Psoas
35	chr5:127297800-127306400	Weak transcription	Right Atrium	heart
36	chr5:127297800-127323200	Weak transcription	Gastric	stomach
37	chr5:127297800-127323600	Weak transcription	HSMMtube	muscle
38	chr5:127297800-127358400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:127298000-127304000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:127298400-127303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:127298400-127303800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:127298400-127304800	Weak transcription	Small Intestine	intestine
43	chr5:127298600-127314400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:127299400-127303800	Weak transcription	NHDF-Ad	bronchial
45	chr5:127300600-127312600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:127301000-127302400	ZNF genes & repeats	GM12878-XiMat	blood
47	chr5:127301800-127302200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:127301800-127302200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr5:127301800-127302200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:127301800-127302200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland

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