Variant report

Variant	rs28579790
Chromosome Location	chr5:177025862-177025863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177024652-177028404	MCF10A-Er-Src	breast:	n/a	n/a
2	NFATC1	chr5:177025469-177025993	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:177025670-177026326	Raji	blood:	n/a	n/a
4	POLR2A	chr5:177025360-177026361	GM12878	blood:	n/a	n/a
5	FOS	chr5:177025478-177025892	HUVEC	blood vessel:	n/a	chr5:177025691-177025702
6	POLR2A	chr5:177025563-177025895	GM12878	blood:	n/a	n/a
7	GABPA	chr5:177025411-177025878	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr5:177025437-177025923	U87	brain:	n/a	n/a
9	POLR2A	chr5:177025374-177025966	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr5:177024558-177028245	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr5:177025492-177026329	HUVEC	blood vessel:	n/a	n/a
12	RCOR1	chr5:177025824-177026065	HepG2	liver:	n/a	n/a
13	GATA2	chr5:177025476-177025942	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr5:177025565-177025918	GM12891	blood:	n/a	n/a
15	BACH1	chr5:177025825-177026017	K562	blood:	n/a	n/a
16	CEBPZ	chr5:177025793-177026307	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:177025523-177028484	HepG2	liver:	n/a	n/a
18	POLR2A	chr5:177025437-177025918	U87	brain:	n/a	n/a
19	POLR2A	chr5:177025345-177025985	GM12891	blood:	n/a	n/a
20	POLR2A	chr5:177025377-177025948	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr5:177025404-177026411	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:177025419-177026373	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:177025307-177026489	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:177025404-177028000	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:177025419-177026240	K562	blood:	n/a	n/a
26	POLR2A	chr5:177025382-177026279	K562	blood:	n/a	n/a
27	POLR2A	chr5:177025378-177025982	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr5:177025389-177026366	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:177025246-177026443	HUVEC	blood vessel:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:176920960..176923857-chr5:177025688..177028389,2	K562	blood:
2	chr5:176920960..176922896-chr5:177025688..177028644,2	K562	blood:
3	chr5:176923252..176925841-chr5:177025670..177028479,3	K562	blood:
4	chr5:177025539..177028252-chr5:177630597..177632555,2	K562	blood:
5	chr5:176980839..176983786-chr5:177025411..177027346,2	MCF-7	breast:
6	chr5:176895756..176898053-chr5:177023963..177026358,2	K562	blood:
7	chr5:176923028..176926285-chr5:177025596..177029619,3	MCF-7	breast:
8	chr5:177025398..177027289-chr5:177540105..177542434,2	MCF-7	breast:
9	chr5:176922985..176925564-chr5:177025681..177028407,2	MCF-7	breast:
10	chr5:177010880..177013120-chr5:177024317..177026904,2	K562	blood:
11	chr5:176942355..176946513-chr5:177025554..177029046,7	MCF-7	breast:

No data

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000272459	Chromatin interaction
ENSG00000248996	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000183258	Chromatin interaction
ENSG00000145911	Chromatin interaction
ENSG00000146067	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10036396	0.81[ASN][1000 genomes]
rs1047577	0.83[ASN][1000 genomes]
rs11490750	0.94[ASN][1000 genomes]
rs12654617	0.84[ASN][1000 genomes]
rs1872623	0.83[ASN][1000 genomes]
rs1872624	0.96[ASN][1000 genomes]
rs1963011	0.81[ASN][1000 genomes]
rs28375402	0.95[ASN][1000 genomes]
rs28707336	0.88[ASN][1000 genomes]
rs28757437	0.94[ASN][1000 genomes]
rs4458584	0.82[ASN][1000 genomes]
rs60992195	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6882209	0.83[ASN][1000 genomes]
rs6889184	0.83[ASN][1000 genomes]
rs7703727	0.80[ASN][1000 genomes]
rs901379	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1022630	chr5:176975746-177028082	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv537966	chr5:176975746-177028082	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177021400-177026200	Weak transcription	Fetal Heart	heart
2	chr5:177021600-177026800	Weak transcription	Fetal Brain Male	brain
3	chr5:177022400-177026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:177022400-177026200	Weak transcription	Fetal Kidney	kidney
5	chr5:177023000-177026000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:177023200-177026200	Weak transcription	Psoas Muscle	Psoas
7	chr5:177023400-177026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:177023400-177026200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:177023400-177026200	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:177023600-177026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:177023600-177026200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:177023800-177026000	Weak transcription	Brain Anterior Caudate	brain
13	chr5:177023800-177026200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:177023800-177026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:177023800-177026200	Weak transcription	Brain Angular Gyrus	brain
16	chr5:177023800-177026200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:177023800-177026200	Weak transcription	Brain Substantia Nigra	brain
18	chr5:177023800-177026200	Weak transcription	Pancreas	Pancrea
19	chr5:177023800-177026200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:177023800-177026200	Weak transcription	NHDF-Ad	bronchial
21	chr5:177023800-177026600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:177023800-177026600	Weak transcription	Aorta	Aorta
23	chr5:177023800-177026600	Weak transcription	Gastric	stomach
24	chr5:177023800-177026600	Weak transcription	HSMM	muscle
25	chr5:177023800-177026600	Weak transcription	HSMMtube	muscle
26	chr5:177024000-177026000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:177024000-177026000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:177024000-177026000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:177024000-177026000	Weak transcription	Right Ventricle	heart
30	chr5:177024000-177026200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:177024000-177026200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:177024000-177026200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:177024000-177026200	Weak transcription	Primary T cells from cord blood	blood
34	chr5:177024000-177026200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:177024000-177026200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:177024000-177026200	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:177024000-177026200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:177024000-177026200	Weak transcription	Colonic Mucosa	Colon
39	chr5:177024000-177026200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:177024000-177026200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:177024000-177026200	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:177024000-177026200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:177024000-177026200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:177024000-177026200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:177024000-177026400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:177024000-177026600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:177024000-177026600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:177024000-177026600	Weak transcription	Esophagus	oesophagus
49	chr5:177024000-177026600	Weak transcription	Fetal Lung	lung
50	chr5:177024000-177026600	Weak transcription	Left Ventricle	heart

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