Variant report

Variant	rs28647448
Chromosome Location	chr5:41942924-41942925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41941926..41943756-chr5:41945285..41947330,2	K562	blood:
2	chr5:41937638..41939431-chr5:41942601..41944162,2	K562	blood:
3	chr5:41925015..41928042-chr5:41941210..41944790,4	K562	blood:
4	chr5:41940424..41943829-chr5:41945093..41947909,5	K562	blood:

Variant related genes	Relation type
ENSG00000151876	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10035434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043371	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10044526	0.88[AMR][1000 genomes]
rs10045473	1.00[EUR][1000 genomes]
rs10051322	1.00[EUR][1000 genomes]
rs10052226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10053522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10054130	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057587	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10059424	0.97[EUR][1000 genomes]
rs10060170	1.00[EUR][1000 genomes]
rs10062703	1.00[EUR][1000 genomes]
rs10064298	1.00[EUR][1000 genomes]
rs10064380	0.95[EUR][1000 genomes]
rs10065016	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10065335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069638	1.00[EUR][1000 genomes]
rs10070201	1.00[EUR][1000 genomes]
rs10075429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10077481	0.95[EUR][1000 genomes]
rs10078011	0.95[EUR][1000 genomes]
rs10079651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1027348	0.95[EUR][1000 genomes]
rs10472357	1.00[EUR][1000 genomes]
rs10472359	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10473252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10473255	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738449	0.82[AMR][1000 genomes]
rs11738956	0.95[EUR][1000 genomes]
rs11742939	0.82[AMR][1000 genomes]
rs11745460	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11745530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11746530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11748933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13355194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13357951	1.00[EUR][1000 genomes]
rs13358459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360765	0.88[AMR][1000 genomes]
rs1567323	1.00[EUR][1000 genomes]
rs16872052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872094	0.85[AMR][1000 genomes]
rs16872097	0.88[AMR][1000 genomes]
rs16872100	0.82[AMR][1000 genomes]
rs17339188	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1813615	0.82[AMR][1000 genomes]
rs1813616	0.82[AMR][1000 genomes]
rs2011105	0.82[AMR][1000 genomes]
rs2113053	0.83[EUR][1000 genomes]
rs2231910	1.00[EUR][1000 genomes]
rs34493032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35890705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4957178	1.00[EUR][1000 genomes]
rs4957180	1.00[EUR][1000 genomes]
rs4957436	1.00[EUR][1000 genomes]
rs4957437	1.00[EUR][1000 genomes]
rs4957438	1.00[EUR][1000 genomes]
rs57944767	0.90[EUR][1000 genomes]
rs582920	0.92[EUR][1000 genomes]
rs583090	0.87[EUR][1000 genomes]
rs584067	0.90[EUR][1000 genomes]
rs590851	0.90[EUR][1000 genomes]
rs591384	0.85[EUR][1000 genomes]
rs602274	0.90[EUR][1000 genomes]
rs61058110	0.95[EUR][1000 genomes]
rs67152480	0.95[EUR][1000 genomes]
rs678061	0.92[EUR][1000 genomes]
rs72746926	0.95[EUR][1000 genomes]
rs72746928	0.95[EUR][1000 genomes]
rs72746930	0.95[EUR][1000 genomes]
rs72746932	0.95[EUR][1000 genomes]
rs72746933	0.93[EUR][1000 genomes]
rs72746952	0.95[EUR][1000 genomes]
rs72746962	0.90[EUR][1000 genomes]
rs72746966	0.95[EUR][1000 genomes]
rs72746968	0.95[EUR][1000 genomes]
rs72746975	0.95[EUR][1000 genomes]
rs72746983	0.95[EUR][1000 genomes]
rs72746985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72746995	1.00[EUR][1000 genomes]
rs72746996	0.95[EUR][1000 genomes]
rs72746997	0.95[EUR][1000 genomes]
rs72746999	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72747000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72747001	1.00[EUR][1000 genomes]
rs72747002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748613	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748620	1.00[EUR][1000 genomes]
rs72748623	0.83[EUR][1000 genomes]
rs72748635	0.85[AMR][1000 genomes]
rs72748641	0.82[AMR][1000 genomes]
rs7341062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723992	1.00[EUR][1000 genomes]
rs9292826	0.95[EUR][1000 genomes]
rs9292828	0.95[EUR][1000 genomes]
rs9292832	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885033	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885117	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs989747	0.82[AMR][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	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
2	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
4	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41926000-41951400	Weak transcription	Gastric	stomach
2	chr5:41926200-41943200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:41926200-41945000	Weak transcription	HSMM	muscle
4	chr5:41926200-41945200	Weak transcription	Esophagus	oesophagus
5	chr5:41926200-41945400	Weak transcription	Fetal Lung	lung
6	chr5:41926200-41946800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:41926200-41947000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:41926800-41946200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:41930600-41943000	Weak transcription	Hela-S3	cervix
10	chr5:41935400-41943000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:41935600-41945600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:41935800-41946000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:41935800-41946200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:41936000-41943200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:41936000-41945200	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:41936000-41946200	Weak transcription	Brain Angular Gyrus	brain
17	chr5:41936200-41943600	Weak transcription	Fetal Thymus	thymus
18	chr5:41936200-41945600	Weak transcription	Placenta	Placenta
19	chr5:41936200-41945600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:41936200-41946600	Weak transcription	Brain Anterior Caudate	brain
21	chr5:41936600-41944800	Weak transcription	Primary T cells from cord blood	blood
22	chr5:41936600-41951400	Weak transcription	Aorta	Aorta
23	chr5:41936600-41951400	Weak transcription	Left Ventricle	heart
24	chr5:41936800-41943000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:41937200-41944400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:41937600-41945600	Weak transcription	Primary B cells from cord blood	blood
27	chr5:41939000-41945200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:41939200-41943600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:41939200-41945000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:41939200-41945400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:41939400-41943800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:41939400-41945000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:41939400-41945400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:41941600-41943200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:41941600-41943400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:41941600-41943800	Weak transcription	Liver	Liver
37	chr5:41941600-41945000	Weak transcription	Dnd41	blood
38	chr5:41942000-41943600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:41942200-41945600	Weak transcription	Adipose Nuclei	Adipose

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