Variant report

Variant	rs56006220
Chromosome Location	chr17:45975989-45975990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr17:45975660-45975991	K562	blood:	n/a	chr17:45975814-45975825 chr17:45975812-45975823

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45974701..45976946-chr17:45989221..45991463,2	MCF-7	breast:
2	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
3	chr17:45909005..45911115-chr17:45973524..45976296,3	MCF-7	breast:
4	chr17:45907865..45909742-chr17:45974096..45976119,2	MCF-7	breast:
5	chr17:45973201..45977546-chr17:46016018..46021091,7	K562	blood:
6	chr17:45973797..45976110-chr17:46092219..46094181,2	MCF-7	breast:
7	chr17:45914563..45916349-chr17:45975385..45977365,2	K562	blood:
8	chr17:45913357..45915949-chr17:45973586..45976163,2	K562	blood:
9	chr17:45895199..45899793-chr17:45971655..45976847,6	K562	blood:
10	chr17:45974878..45977034-chr17:46001885..46004238,2	K562	blood:
11	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
12	chr17:45973858..45976253-chr17:46007245..46011089,3	K562	blood:
13	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
14	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
15	chr17:45975938..45978539-chr17:45995785..45997844,2	MCF-7	breast:
16	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:
17	chr17:45909200..45911562-chr17:45975742..45978250,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRR15L-5	chr17:45975826-45976669	ENSG00000234494.2
2	lnc-PRR15L-5	chr17:45975752-45977744	NONHSAT054343
3	lnc-PRR15L-5	chr17:45975640-45976669	ENSG00000234494.3
4	lnc-PRR15L-5	chr17:45975752-45976669	NONHSAT054344

No data

Variant related genes	Relation type
ENSG00000264920	TF binding region
ENSG00000266601	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1133221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12232488	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12453773	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16949270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16949296	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16949427	0.91[ASN][1000 genomes]
rs16949651	0.85[ASN][1000 genomes]
rs17616799	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1986694	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2325750	0.84[ASN][1000 genomes]
rs3764393	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4450442	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4614773	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55956628	0.92[ASN][1000 genomes]
rs56124407	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56218899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56402159	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs57782323	0.91[AFR][1000 genomes]
rs58695897	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61396871	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61702159	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7213084	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7214154	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7217147	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73323310	0.92[ASN][1000 genomes]
rs8082055	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9944405	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974200-45976400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr17:45974200-45982800	Weak transcription	Spleen	Spleen
3	chr17:45974400-45978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:45974600-45977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:45974600-45977000	Weak transcription	Lung	lung
6	chr17:45974600-45979000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:45974600-45981600	Weak transcription	Pancreas	Pancrea
8	chr17:45974600-45981800	Weak transcription	Ovary	ovary
9	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:45974800-45976200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr17:45974800-45976400	Enhancers	Aorta	Aorta
12	chr17:45974800-45976600	Weak transcription	Right Ventricle	heart
13	chr17:45974800-45977400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:45974800-45978800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:45975000-45976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:45975000-45976000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:45975000-45976200	Enhancers	Primary B cells from cord blood	blood
18	chr17:45975000-45976200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:45975000-45976400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:45975000-45976800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:45975000-45976800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr17:45975000-45976800	Weak transcription	Fetal Intestine Small	intestine
23	chr17:45975000-45976800	Weak transcription	NHDF-Ad	bronchial
24	chr17:45975000-45977000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:45975000-45977000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:45975000-45977000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:45975000-45977000	Enhancers	Colon Smooth Muscle	Colon
28	chr17:45975000-45977400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr17:45975000-45977800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:45975000-45978000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:45975000-45978800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr17:45975000-45982000	Weak transcription	Esophagus	oesophagus
33	chr17:45975000-45982200	Weak transcription	Colonic Mucosa	Colon
34	chr17:45975000-45982800	Weak transcription	Gastric	stomach
35	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:45975200-45976000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:45975200-45976000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:45975200-45976000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr17:45975200-45976000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr17:45975200-45976200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr17:45975200-45976200	Weak transcription	HepG2	liver
42	chr17:45975200-45976400	Enhancers	Brain Substantia Nigra	brain
43	chr17:45975200-45976800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr17:45975200-45976800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:45975200-45976800	Weak transcription	Liver	Liver
46	chr17:45975200-45977000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:45975200-45977000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:45975200-45977000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr17:45975200-45977200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:45975200-45977400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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