Variant report

Variant	rs4865547
Chromosome Location	chr5:52862825-52862826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52861548..52863990-chr5:52926971..52929955,2	MCF-7	breast:
2	chr5:52851780..52858194-chr5:52858438..52864794,9	MCF-7	breast:
3	chr5:52855191..52856804-chr5:52862237..52864933,2	K562	blood:
4	chr5:52855304..52857106-chr5:52862237..52863939,3	K562	blood:

Variant related genes	Relation type
ENSG00000164258	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10036570	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10065003	0.94[ASN][1000 genomes]
rs10068241	0.80[EUR][1000 genomes]
rs10078892	0.86[ASN][1000 genomes]
rs10471866	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940322	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940323	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940328	0.89[EUR][1000 genomes]
rs10940330	0.87[EUR][1000 genomes]
rs12514280	0.85[ASN][1000 genomes]
rs12654088	0.90[EUR][1000 genomes]
rs12657948	0.89[ASN][1000 genomes]
rs13164833	0.83[ASN][1000 genomes]
rs13176154	0.87[EUR][1000 genomes]
rs13177321	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13179304	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13190280	0.85[EUR][1000 genomes]
rs1532162	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881474	0.94[ASN][1000 genomes]
rs171740	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1844697	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1873426	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs187658	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs189848	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs189849	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs194364	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256081	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256082	0.88[ASN][1000 genomes]
rs256086	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs256093	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256096	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs256098	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256099	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256109	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256111	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256118	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256119	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2607476	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2607477	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2607478	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2607482	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2607483	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2607485	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2607503	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2607506	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2607508	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2607510	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2637002	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2637029	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2655381	0.90[EUR][1000 genomes]
rs3103597	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3103598	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3103600	0.82[AFR][1000 genomes]
rs3103601	0.82[ASN][1000 genomes]
rs31308	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34071992	0.88[ASN][1000 genomes]
rs365358	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs365932	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs366313	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs368461	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs371123	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs372215	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377077	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs377159	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs381575	0.84[ASN][1000 genomes]
rs388311	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392169	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs401967	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs402751	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs404838	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs409313	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4147732	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147734	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs417550	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425085	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs42565	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs425880	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs426196	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs432020	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs438736	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs443254	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs444848	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs445347	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs449208	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451591	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451881	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454735	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865548	0.99[ASN][1000 genomes]
rs499760	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs524289	0.92[ASN][1000 genomes]
rs535277	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58889983	0.91[ASN][1000 genomes]
rs693204	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711180	0.99[ASN][1000 genomes]
rs7717681	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7736747	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786330	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs786331	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs786334	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs918625	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923610	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292024	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9790964	0.94[ASN][1000 genomes]
rs9791019	0.92[ASN][1000 genomes]
rs9791152	0.94[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:68 , 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	chr5:52857600-52864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:52857600-52875000	Weak transcription	Thymus	Thymus
5	chr5:52857800-52863000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:52857800-52864400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:52857800-52864400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
9	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
11	chr5:52857800-52898800	Weak transcription	HSMM	muscle
12	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:52858000-52864800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:52858000-52865000	Weak transcription	HMEC	breast
16	chr5:52858000-52865800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:52858000-52868800	Weak transcription	Psoas Muscle	Psoas
18	chr5:52858000-52870800	Weak transcription	Primary T cells from cord blood	blood
19	chr5:52858000-52870800	Weak transcription	Ovary	ovary
20	chr5:52858000-52870800	Weak transcription	Right Ventricle	heart
21	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
23	chr5:52858200-52863200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:52858200-52864000	Weak transcription	NHDF-Ad	bronchial
25	chr5:52858200-52864200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:52858200-52864800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:52858200-52867400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:52858200-52867600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:52858200-52880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:52858200-52897200	Weak transcription	NHEK	skin
32	chr5:52858400-52864200	Weak transcription	Fetal Stomach	stomach
33	chr5:52858400-52864400	Weak transcription	A549	lung
34	chr5:52858400-52864600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:52858400-52870800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr5:52858600-52864000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:52858600-52865200	Weak transcription	GM12878-XiMat	blood
40	chr5:52858600-52867000	Weak transcription	Brain Angular Gyrus	brain
41	chr5:52859400-52864800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:52859600-52867600	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:52859800-52864600	Weak transcription	Brain Germinal Matrix	brain
44	chr5:52860000-52863400	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr5:52860000-52870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
47	chr5:52860200-52863400	Weak transcription	Fetal Heart	heart
48	chr5:52860200-52864200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:52860200-52864600	Weak transcription	HepG2	liver
50	chr5:52860200-52864800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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