Variant report

Variant	rs55656553
Chromosome Location	chr17:38480006-38480007
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38331383..38339312-chr17:38470464..38480799,28	MCF-7	breast:
2	chr17:38447259..38448937-chr17:38479509..38481523,2	K562	blood:
3	chr17:38478697..38480304-chr17:39940494..39943050,2	MCF-7	breast:
4	chr17:38479395..38482301-chr17:38490961..38492662,2	K562	blood:
5	chr17:38475685..38480356-chr17:38717204..38721224,4	MCF-7	breast:
6	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
7	chr17:38472788..38480698-chr17:38493295..38509406,39	K562	blood:

Variant related genes	Relation type
ENSG00000126353	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000173801	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000094804	Chromatin interaction
ENSG00000265666	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11078939	0.86[AMR][1000 genomes]
rs11078940	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12051734	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12103711	0.96[ASN][1000 genomes]
rs12946680	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13706	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16965687	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1807273	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2077464	0.93[ASN][1000 genomes]
rs2120200	0.96[ASN][1000 genomes]
rs28537537	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28663197	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35286757	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36030243	0.96[ASN][1000 genomes]
rs4077125	0.86[AMR][1000 genomes]
rs4134994	0.90[ASN][1000 genomes]
rs4566234	0.86[AMR][1000 genomes]
rs56029626	0.81[AMR][1000 genomes]
rs57179137	0.93[ASN][1000 genomes]
rs58822685	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59406133	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59490243	0.86[AMR][1000 genomes]
rs60220138	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7217852	0.95[ASN][1000 genomes]
rs72836635	0.83[AMR][1000 genomes]
rs72836636	0.80[EUR][1000 genomes]
rs72836639	0.80[EUR][1000 genomes]
rs72836641	0.80[EUR][1000 genomes]
rs72836642	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72836648	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72836651	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72836653	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72836656	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72836660	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7359537	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73983025	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8080931	0.83[AMR][1000 genomes]
rs9303285	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303286	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891694	0.86[AMR][1000 genomes]
rs9892404	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9892946	0.86[AMR][1000 genomes]
rs9893520	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9894625	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9896312	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9897092	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9904270	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9906409	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9908257	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9914531	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9916460	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9916782	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv1825614	chr17:38466377-38481100	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1063310	chr17:38467043-38499351	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38472200-38480800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr17:38473200-38481000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr17:38473200-38481200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr17:38473400-38481200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:38473800-38480600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr17:38474800-38481000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr17:38474800-38487000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr17:38475000-38481000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr17:38475400-38480600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr17:38475400-38481000	Flanking Active TSS	Osteobl	bone
11	chr17:38475600-38480800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr17:38475600-38482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:38475600-38484600	Enhancers	Placenta	Placenta
14	chr17:38475600-38484600	Enhancers	Spleen	Spleen
15	chr17:38475600-38484800	Enhancers	Stomach Mucosa	stomach
16	chr17:38476200-38480800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr17:38476200-38481000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:38476200-38481000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr17:38476200-38481000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr17:38476200-38481000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr17:38476200-38481000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr17:38476200-38481200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:38476200-38481200	Flanking Active TSS	GM12878-XiMat	blood
24	chr17:38476200-38485000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr17:38476400-38481200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:38476600-38480600	Flanking Active TSS	Colonic Mucosa	Colon
27	chr17:38476600-38480800	Enhancers	Pancreas	Pancrea
28	chr17:38476600-38481200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:38476800-38480400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:38477000-38480400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr17:38477600-38484800	Enhancers	Ovary	ovary
32	chr17:38477800-38480200	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr17:38478200-38480400	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr17:38478200-38480800	Enhancers	Brain Germinal Matrix	brain
35	chr17:38478400-38480200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:38478400-38483200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:38478600-38481200	Enhancers	Gastric	stomach
38	chr17:38478600-38482600	Weak transcription	Aorta	Aorta
39	chr17:38478800-38483400	Enhancers	Hela-S3	cervix
40	chr17:38478800-38484600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr17:38478800-38484600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr17:38478800-38484600	Enhancers	Small Intestine	intestine
43	chr17:38479000-38480400	Enhancers	HMEC	breast
44	chr17:38479000-38481200	Enhancers	Esophagus	oesophagus
45	chr17:38479000-38482800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:38479000-38483800	Genic enhancers	Fetal Stomach	stomach
47	chr17:38479000-38484200	Genic enhancers	Fetal Intestine Small	intestine
48	chr17:38479000-38484600	Enhancers	Lung	lung
49	chr17:38479000-38485000	Enhancers	Psoas Muscle	Psoas
50	chr17:38479200-38480200	Flanking Active TSS	Primary B cells from cord blood	blood

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