Variant report

Variant	rs1552649
Chromosome Location	chr5:52870476-52870477
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	chr5:52870145..52872320-chr5:52872333..52875055,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10072971	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10077935	0.83[ASN][1000 genomes]
rs1030228	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12521381	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1465445	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1532163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173905	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1844696	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844698	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs187659	0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs198941	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2130744	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256083	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256085	0.80[CHB][hapmap];0.86[ASN][1000 genomes]
rs256087	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256090	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256097	0.81[ASN][1000 genomes]
rs256107	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256110	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256112	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256113	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs256116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256117	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2607501	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2607502	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607509	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2607511	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2636991	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2636999	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2637004	0.80[CHB][hapmap];0.86[ASN][1000 genomes]
rs2637027	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2637030	0.81[ASN][1000 genomes]
rs271213	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs271217	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs31302	0.81[ASN][1000 genomes]
rs31303	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs370594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372006	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372135	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs375956	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376566	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs381374	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs399141	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs403207	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147740	0.94[CEU][hapmap]
rs423014	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs423872	0.82[ASN][1000 genomes]
rs424955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429384	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430427	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs435187	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs439552	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439641	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs449160	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549131	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6881928	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7728496	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7731940	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs786333	0.81[ASN][1000 genomes]
rs786335	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs813301	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs889291	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs889292	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs923609	0.94[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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:59 , 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	chr5:52857600-52875000	Weak transcription	Thymus	Thymus
4	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
5	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
7	chr5:52857800-52898800	Weak transcription	HSMM	muscle
8	chr5:52858000-52870800	Weak transcription	Primary T cells from cord blood	blood
9	chr5:52858000-52870800	Weak transcription	Ovary	ovary
10	chr5:52858000-52870800	Weak transcription	Right Ventricle	heart
11	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
13	chr5:52858200-52880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:52858200-52897200	Weak transcription	NHEK	skin
16	chr5:52858400-52870800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:52860000-52870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
21	chr5:52860200-52885600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:52860600-52884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:52861600-52873000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:52861600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:52863000-52870600	Weak transcription	Left Ventricle	heart
26	chr5:52865000-52872800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr5:52865000-52900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:52865200-52885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:52865600-52870800	Weak transcription	HepG2	liver
30	chr5:52865600-52871600	Weak transcription	Liver	Liver
31	chr5:52865600-52871800	Weak transcription	A549	lung
32	chr5:52865600-52872400	Weak transcription	Stomach Mucosa	stomach
33	chr5:52865600-52883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:52865600-52898400	Weak transcription	Fetal Lung	lung
35	chr5:52865600-52899800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:52866200-52883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:52866400-52884200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:52867600-52870600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:52867600-52870800	Weak transcription	Brain Substantia Nigra	brain
40	chr5:52867600-52888400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:52867800-52871600	Weak transcription	Fetal Heart	heart
42	chr5:52867800-52872600	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:52867800-52874200	Weak transcription	Brain Angular Gyrus	brain
44	chr5:52868200-52871600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:52868200-52872200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:52868200-52873800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:52868200-52885200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:52868400-52882000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:52868600-52870800	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:52869200-52870600	Weak transcription	Psoas Muscle	Psoas

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