Variant report

Variant	rs657796
Chromosome Location	chr5:52020391-52020392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12332623	0.95[ASN][1000 genomes]
rs1626287	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645393	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645394	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164611	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs164612	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1668506	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs244481	0.90[ASN][1000 genomes]
rs244491	0.85[ASN][1000 genomes]
rs244493	0.88[ASN][1000 genomes]
rs244495	0.86[ASN][1000 genomes]
rs29976	0.88[ASN][1000 genomes]
rs29977	0.90[ASN][1000 genomes]
rs29980	0.89[ASN][1000 genomes]
rs29982	0.90[ASN][1000 genomes]
rs351933	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351937	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351940	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs39811	0.93[ASN][1000 genomes]
rs599698	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651393	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs658771	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664248	0.83[AMR][1000 genomes];0.95[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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52019800-52021000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:52019800-52021000	Enhancers	Dnd41	blood
3	chr5:52019800-52021400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr5:52019800-52021600	Enhancers	Primary T cells from cord blood	blood
5	chr5:52019800-52021600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:52019800-52021600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:52019800-52023400	Enhancers	Hela-S3	cervix
8	chr5:52019800-52023800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:52019800-52024000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr5:52019800-52025000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:52019800-52025200	Enhancers	Fetal Thymus	thymus
12	chr5:52020000-52020600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:52020000-52021000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:52020000-52021200	Enhancers	Duodenum Mucosa	Duodenum
15	chr5:52020000-52021400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:52020000-52021800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:52020000-52022600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:52020000-52023800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:52020000-52023800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:52020000-52025200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:52020200-52021400	Weak transcription	Small Intestine	intestine
22	chr5:52020200-52021600	Enhancers	HMEC	breast
23	chr5:52020200-52022000	Enhancers	Fetal Intestine Large	intestine
24	chr5:52020200-52022400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr5:52020200-52022800	Enhancers	HepG2	liver

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