Variant report

Variant	rs256108
Chromosome Location	chr5:52874253-52874254
allele	C/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: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10072971	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10077935	0.83[ASN][1000 genomes]
rs1030228	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12521381	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1465445	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1532163	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1552649	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1559266	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs173905	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1844696	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844698	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs187659	0.84[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs198941	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2130744	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279516	0.91[YRI][hapmap]
rs256083	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256085	0.87[ASN][1000 genomes]
rs256087	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256090	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256095	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256097	0.82[ASN][1000 genomes]
rs256107	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256110	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256112	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256113	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256116	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256117	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607501	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607502	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2607509	0.82[ASN][1000 genomes]
rs2607511	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636991	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636999	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2637004	0.87[ASN][1000 genomes]
rs2637027	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2637030	0.82[ASN][1000 genomes]
rs271213	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs271217	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs31302	0.82[ASN][1000 genomes]
rs31303	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs370594	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372006	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372135	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs375956	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376566	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs381374	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399141	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs403207	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147740	0.88[CEU][hapmap]
rs423014	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs423872	0.83[ASN][1000 genomes]
rs424955	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429384	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs430427	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435187	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439552	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs439641	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs449160	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549131	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881928	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7728496	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7731940	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs786333	0.82[ASN][1000 genomes]
rs786335	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs813301	0.82[ASN][1000 genomes]
rs889291	0.89[JPT][hapmap]
rs889292	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs923609	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	chr5:52857600-52875000	Weak transcription	Thymus	Thymus
2	chr5:52857800-52883000	Weak transcription	Hela-S3	cervix
3	chr5:52857800-52884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
5	chr5:52857800-52898800	Weak transcription	HSMM	muscle
6	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
8	chr5:52858200-52880400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:52858200-52897200	Weak transcription	NHEK	skin
11	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
14	chr5:52860200-52885600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:52860600-52884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:52861600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:52865000-52900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:52865200-52885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:52865600-52883400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:52865600-52898400	Weak transcription	Fetal Lung	lung
21	chr5:52865600-52899800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr5:52866200-52883400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:52866400-52884200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:52867600-52888400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:52868200-52885200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:52868400-52882000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:52869600-52896000	Weak transcription	Fetal Stomach	stomach
28	chr5:52870200-52892000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:52870600-52875600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr5:52870800-52874600	Enhancers	HepG2	liver
31	chr5:52870800-52876400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:52871000-52875000	Weak transcription	Adipose Nuclei	Adipose
33	chr5:52871000-52881400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:52871200-52877800	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:52872000-52892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:52872200-52885000	Weak transcription	Primary T cells from cord blood	blood
37	chr5:52872400-52874400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr5:52872600-52875000	Enhancers	Colon Smooth Muscle	Colon
39	chr5:52873000-52874600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:52873000-52884800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:52873000-52887000	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:52873000-52889200	Weak transcription	A549	lung
43	chr5:52873000-52900400	Weak transcription	Gastric	stomach
44	chr5:52873200-52899000	Weak transcription	Right Atrium	heart
45	chr5:52873400-52874800	Weak transcription	Psoas Muscle	Psoas
46	chr5:52873400-52876800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:52873400-52878200	Weak transcription	Right Ventricle	heart
48	chr5:52873400-52885400	Weak transcription	Left Ventricle	heart
49	chr5:52873400-52889800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:52873800-52874800	Enhancers	Rectal Smooth Muscle	rectum

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