Variant report

Variant	rs7731940
Chromosome Location	chr5:52863638-52863639
allele	A/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: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10072971	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10077935	0.87[ASN][1000 genomes]
rs1030228	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12521381	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1465445	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552649	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559266	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173905	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1844696	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1844698	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs187659	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs198941	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2130744	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256083	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256085	0.83[ASN][1000 genomes]
rs256087	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256090	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256095	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256107	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256108	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256112	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256113	0.87[ASN][1000 genomes]
rs256116	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256117	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607501	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607502	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2607511	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636991	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2636999	0.81[AMR][1000 genomes]
rs2637004	0.83[ASN][1000 genomes]
rs2637027	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs271213	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs271217	0.84[ASN][1000 genomes]
rs31303	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs370594	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs372006	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs372135	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs375956	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376566	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs381374	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs403207	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs423014	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs424955	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs429384	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs430427	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs435187	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439552	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs449160	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs549131	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6881928	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7728496	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs786335	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889292	0.94[EUR][1000 genomes]
rs923609	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[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:67 , 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	chr5:52857800-52864400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:52857800-52864400	Weak transcription	Fetal Intestine Small	intestine
7	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
8	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
10	chr5:52857800-52898800	Weak transcription	HSMM	muscle
11	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:52858000-52864600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:52858000-52864800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:52858000-52865000	Weak transcription	HMEC	breast
15	chr5:52858000-52865800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:52858000-52868800	Weak transcription	Psoas Muscle	Psoas
17	chr5:52858000-52870800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:52858000-52870800	Weak transcription	Ovary	ovary
19	chr5:52858000-52870800	Weak transcription	Right Ventricle	heart
20	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
22	chr5:52858200-52864000	Weak transcription	NHDF-Ad	bronchial
23	chr5:52858200-52864200	Weak transcription	Adipose Nuclei	Adipose
24	chr5:52858200-52864800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:52858200-52867400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:52858200-52867600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:52858200-52880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:52858200-52897200	Weak transcription	NHEK	skin
30	chr5:52858400-52864200	Weak transcription	Fetal Stomach	stomach
31	chr5:52858400-52864400	Weak transcription	A549	lung
32	chr5:52858400-52864600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:52858400-52870800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:52858600-52864000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:52858600-52865200	Weak transcription	GM12878-XiMat	blood
38	chr5:52858600-52867000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:52859400-52864800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:52859600-52867600	Weak transcription	Brain Hippocampus Middle	brain
41	chr5:52859800-52864600	Weak transcription	Brain Germinal Matrix	brain
42	chr5:52860000-52870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
44	chr5:52860200-52864200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr5:52860200-52864600	Weak transcription	HepG2	liver
46	chr5:52860200-52864800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:52860200-52865200	Weak transcription	Stomach Mucosa	stomach
48	chr5:52860200-52867200	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:52860200-52867400	Weak transcription	Brain Anterior Caudate	brain
50	chr5:52860200-52867600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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