Variant report

Variant	rs10940322
Chromosome Location	chr5:52858919-52858920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52855491..52857473-chr5:52858185..52859703,2	MCF-7	breast:
2	chr5:52858854..52861653-chr5:52864359..52868454,4	MCF-7	breast:
3	chr5:52851780..52858194-chr5:52858438..52864794,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164258	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10065003	0.91[ASN][1000 genomes]
rs10078892	0.83[ASN][1000 genomes]
rs10471866	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10940323	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940328	0.84[EUR][1000 genomes]
rs10940330	0.82[EUR][1000 genomes]
rs12514280	0.82[ASN][1000 genomes]
rs12654088	0.85[EUR][1000 genomes]
rs12657948	0.86[ASN][1000 genomes]
rs13176154	0.82[EUR][1000 genomes]
rs13177321	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13179304	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1532162	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16881474	0.91[ASN][1000 genomes]
rs171740	0.83[EUR][1000 genomes]
rs1844697	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1873426	0.85[EUR][1000 genomes]
rs187658	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs189848	0.85[EUR][1000 genomes]
rs189849	0.85[EUR][1000 genomes]
rs194364	0.84[EUR][1000 genomes]
rs256081	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256082	0.85[ASN][1000 genomes]
rs256086	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs256093	0.85[EUR][1000 genomes]
rs256096	0.85[EUR][1000 genomes]
rs256098	0.85[EUR][1000 genomes]
rs256099	0.83[EUR][1000 genomes]
rs256109	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256111	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256118	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256119	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607476	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607477	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607478	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607483	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607485	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2607503	0.85[EUR][1000 genomes]
rs2607506	0.85[EUR][1000 genomes]
rs2607508	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607510	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2637002	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2637029	0.85[EUR][1000 genomes]
rs2655381	0.85[EUR][1000 genomes]
rs3103597	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103598	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs31308	0.85[EUR][1000 genomes]
rs34071992	0.85[ASN][1000 genomes]
rs365358	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs365932	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs366313	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs368461	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs371123	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs372215	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs377077	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs377159	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs381575	0.81[ASN][1000 genomes]
rs388311	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs392169	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs401967	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs402751	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs404838	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4147732	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147734	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs417550	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs425085	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42565	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs425880	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs426196	0.85[EUR][1000 genomes]
rs432020	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs438736	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs443254	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs444848	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445347	0.85[EUR][1000 genomes]
rs449208	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs451591	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs451881	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs454735	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4865547	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865548	0.96[ASN][1000 genomes]
rs499760	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs524289	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs535277	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58889983	0.88[ASN][1000 genomes]
rs693204	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7711180	0.96[ASN][1000 genomes]
rs7717681	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7736747	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs786330	0.85[EUR][1000 genomes]
rs786331	0.85[EUR][1000 genomes]
rs786334	0.83[ASN][1000 genomes]
rs918625	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923610	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9790964	0.91[ASN][1000 genomes]
rs9791019	0.89[ASN][1000 genomes]
rs9791152	0.91[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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52857000-52859400	Weak transcription	Spleen	Spleen
2	chr5:52857200-52860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:52857200-52860400	Weak transcription	Pancreas	Pancrea
4	chr5:52857200-52872800	Weak transcription	Gastric	stomach
5	chr5:52857200-52872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:52857400-52859600	Weak transcription	Stomach Mucosa	stomach
7	chr5:52857400-52860200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr5:52857400-52860400	Enhancers	Liver	Liver
9	chr5:52857600-52859000	Enhancers	Brain Hippocampus Middle	brain
10	chr5:52857600-52860000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:52857600-52861000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:52857600-52864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:52857600-52875000	Weak transcription	Thymus	Thymus
14	chr5:52857800-52859400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:52857800-52859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:52857800-52860000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:52857800-52860400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr5:52857800-52860600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr5:52857800-52860800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:52857800-52863000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:52857800-52864400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:52857800-52864400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
24	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
26	chr5:52857800-52898800	Weak transcription	HSMM	muscle
27	chr5:52858000-52859200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:52858000-52859200	Weak transcription	Brain Germinal Matrix	brain
29	chr5:52858000-52860200	Weak transcription	Esophagus	oesophagus
30	chr5:52858000-52860400	Weak transcription	Lung	lung
31	chr5:52858000-52860400	Weak transcription	Right Atrium	heart
32	chr5:52858000-52860600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:52858000-52862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:52858000-52862600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:52858000-52864800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:52858000-52865000	Weak transcription	HMEC	breast
39	chr5:52858000-52865800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:52858000-52868800	Weak transcription	Psoas Muscle	Psoas
41	chr5:52858000-52870800	Weak transcription	Primary T cells from cord blood	blood
42	chr5:52858000-52870800	Weak transcription	Ovary	ovary
43	chr5:52858000-52870800	Weak transcription	Right Ventricle	heart
44	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
46	chr5:52858200-52859200	Weak transcription	Left Ventricle	heart
47	chr5:52858200-52859200	Weak transcription	Small Intestine	intestine
48	chr5:52858200-52859400	Weak transcription	Fetal Heart	heart
49	chr5:52858200-52859600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:52858200-52859600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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