Variant report

Variant	rs16880238
Chromosome Location	chr5:52082563-52082564
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:52082482-52083223	HCT-116	colon:	n/a	n/a
2	CTCF	chr5:52082554-52083136	HCT-116	colon:	n/a	n/a
3	ZEB1	chr5:52082534-52083160	HepG2	liver:	n/a	n/a
4	RAD21	chr5:52082509-52083164	HCT-116	colon:	n/a	n/a
5	RAD21	chr5:52082530-52083206	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:51989244..51989789-chr5:52082448..52083316,3	MCF-7	breast:
2	chr5:52082533..52083427-chr5:52240291..52241141,2	MCF-7	breast:
3	chr5:52082422..52083413-chr5:52210723..52211912,23	MCF-7	breast:
4	chr5:52082398..52083133-chr5:52210696..52211846,7	MCF-7	breast:

Variant related genes	Relation type
ITGA1	TF binding region
PELO	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1363959	0.82[ASN][1000 genomes]
rs1363960	0.82[ASN][1000 genomes]
rs1363961	0.82[ASN][1000 genomes]
rs16880266	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833883	0.81[ASN][1000 genomes]
rs2133476	0.85[ASN][1000 genomes]
rs2173525	0.85[ASN][1000 genomes]
rs2245991	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2245997	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2456210	1.00[YRI][hapmap]
rs2548503	0.82[ASN][1000 genomes]
rs2548504	0.82[ASN][1000 genomes]
rs2548505	0.82[ASN][1000 genomes]
rs2548506	0.82[ASN][1000 genomes]
rs2648732	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2648733	0.82[ASN][1000 genomes]
rs2648734	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2648735	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2648736	1.00[EUR][1000 genomes]
rs2936573	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3096173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1024123	chr5:52052104-52089545	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020640	chr5:52058830-52120858	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52079800-52082600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:52079800-52082600	Weak transcription	NHLF	lung
3	chr5:52079800-52082600	Weak transcription	Osteobl	bone
4	chr5:52080000-52082600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:52080000-52082600	Weak transcription	HMEC	breast
6	chr5:52080000-52082600	Weak transcription	HSMMtube	muscle
7	chr5:52080000-52082800	Weak transcription	HSMM	muscle
8	chr5:52080200-52082600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:52080200-52082600	Weak transcription	Hela-S3	cervix
10	chr5:52081000-52082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:52081000-52082600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:52081000-52082600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:52081000-52082800	Weak transcription	NH-A	brain
14	chr5:52081600-52082600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:52081600-52082800	Weak transcription	Left Ventricle	heart
16	chr5:52081600-52082800	Weak transcription	Small Intestine	intestine
17	chr5:52082200-52082600	Enhancers	Duodenum Mucosa	Duodenum
18	chr5:52082200-52082600	Enhancers	Fetal Kidney	kidney
19	chr5:52082200-52082600	Enhancers	Fetal Lung	lung
20	chr5:52082200-52082600	Enhancers	HepG2	liver
21	chr5:52082200-52082800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:52082200-52082800	Enhancers	Liver	Liver
23	chr5:52082200-52082800	Bivalent Enhancer	A549	lung
24	chr5:52082200-52082800	Enhancers	NHDF-Ad	bronchial
25	chr5:52082200-52083000	Enhancers	NHEK	skin
26	chr5:52082200-52083200	Enhancers	HUVEC	blood vessel
27	chr5:52082400-52082600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:52082400-52082600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:52082400-52082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:52082400-52082600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr5:52082400-52082600	Enhancers	Adipose Nuclei	Adipose
32	chr5:52082400-52082600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr5:52082400-52082600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr5:52082400-52082600	Enhancers	Dnd41	blood
35	chr5:52082400-52082800	Enhancers	Primary T cells from cord blood	blood
36	chr5:52082400-52082800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:52082400-52082800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:52082400-52082800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:52082400-52082800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
40	chr5:52082400-52082800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:52082400-52082800	Enhancers	Fetal Intestine Large	intestine
42	chr5:52082400-52083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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