Variant report

Variant	rs256993
Chromosome Location	chr5:114912024-114912025
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	chr5:114903873..114906375-chr5:114910655..114912171,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-11	chr5:114910746-114913269	NONHSAT103306

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10055677	0.92[EUR][1000 genomes]
rs12187973	0.85[ASN][1000 genomes]
rs13164545	0.87[EUR][1000 genomes]
rs13186296	0.90[EUR][1000 genomes]
rs171774	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs173965	0.96[ASN][1000 genomes]
rs173966	0.99[ASN][1000 genomes]
rs187682	0.83[ASN][1000 genomes]
rs2169771	0.83[ASN][1000 genomes]
rs2303747	0.87[EUR][1000 genomes]
rs2546486	0.84[ASN][1000 genomes]
rs2559990	0.85[ASN][1000 genomes]
rs256942	0.95[EUR][1000 genomes]
rs256943	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs256944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256945	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256947	0.92[EUR][1000 genomes]
rs256948	0.92[EUR][1000 genomes]
rs256949	0.92[EUR][1000 genomes]
rs256950	0.92[EUR][1000 genomes]
rs256951	0.92[EUR][1000 genomes]
rs256952	0.92[EUR][1000 genomes]
rs256953	0.92[EUR][1000 genomes]
rs256954	0.92[EUR][1000 genomes]
rs256964	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs256967	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs256968	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs256969	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256970	0.94[ASN][1000 genomes]
rs256971	0.94[ASN][1000 genomes]
rs256972	0.94[ASN][1000 genomes]
rs256978	0.90[ASN][1000 genomes]
rs256980	0.84[ASN][1000 genomes]
rs256984	0.95[ASN][1000 genomes]
rs256986	0.96[ASN][1000 genomes]
rs256987	0.99[ASN][1000 genomes]
rs256988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256994	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256996	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256997	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256998	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377290	0.95[EUR][1000 genomes]
rs3822579	0.91[EUR][1000 genomes]
rs387718	0.85[ASN][1000 genomes]
rs400570	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs413059	0.91[EUR][1000 genomes]
rs415577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4920967	0.89[EUR][1000 genomes]
rs698366	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs698367	0.92[EUR][1000 genomes]
rs7702283	0.91[EUR][1000 genomes]
rs7702869	0.92[EUR][1000 genomes]
rs7702881	0.92[EUR][1000 genomes]
rs790825	0.95[EUR][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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:114907800-114918200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:114908200-114918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:114908400-114912400	Enhancers	NHDF-Ad	bronchial
5	chr5:114908600-114912200	Enhancers	Osteobl	bone
6	chr5:114908800-114915200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:114908800-114918600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:114909000-114914400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:114909000-114914400	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:114909000-114914600	Weak transcription	Brain Anterior Caudate	brain
11	chr5:114909000-114914800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:114909000-114918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:114909000-114919200	Weak transcription	Left Ventricle	heart
14	chr5:114909000-114919200	Weak transcription	Psoas Muscle	Psoas
15	chr5:114909200-114912800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:114910200-114912200	Enhancers	NHEK	skin
17	chr5:114910200-114918400	Weak transcription	Fetal Intestine Large	intestine
18	chr5:114910400-114914400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:114910400-114914600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:114910400-114925200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:114910400-114929400	Weak transcription	Adipose Nuclei	Adipose
22	chr5:114910800-114916600	Weak transcription	Ovary	ovary
23	chr5:114911000-114912200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:114911000-114912200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:114911000-114912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:114911000-114912200	Enhancers	HMEC	breast
27	chr5:114911000-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:114911000-114912400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:114911000-114912600	Genic enhancers	HSMM	muscle
30	chr5:114911200-114912200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:114911200-114912200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:114911200-114912400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:114911200-114912600	Enhancers	NHLF	lung
35	chr5:114911200-114913600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:114911200-114935600	Weak transcription	Gastric	stomach
37	chr5:114911400-114912400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr5:114911400-114912600	Enhancers	HUVEC	blood vessel
39	chr5:114911400-114917000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:114911600-114912200	Enhancers	NH-A	brain
41	chr5:114911600-114913400	ZNF genes & repeats	GM12878-XiMat	blood
42	chr5:114911600-114913400	Weak transcription	Hela-S3	cervix
43	chr5:114911600-114914400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:114911600-114918600	Weak transcription	HSMMtube	muscle
45	chr5:114911800-114922400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:114912000-114913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:114912000-114915000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:114912000-114924600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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