Variant report

Variant	rs28595585
Chromosome Location	chr5:177025595-177025596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 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	chr5:177025360-177026361	GM12878	blood:	n/a	n/a
4	FOS	chr5:177025478-177025892	HUVEC	blood vessel:	n/a	chr5:177025691-177025702
5	POLR2A	chr5:177025487-177025719	GM12878	blood:	n/a	n/a
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	JUND	chr5:177025502-177025861	K562	blood:	n/a	n/a
9	POLR2A	chr5:177025437-177025923	U87	brain:	n/a	n/a
10	FOS	chr5:177025539-177025817	MCF10A-Er-Src	breast:	n/a	chr5:177025691-177025702
11	POLR2A	chr5:177025394-177025838	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:177025374-177025966	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr5:177024558-177028245	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr5:177025492-177026329	HUVEC	blood vessel:	n/a	n/a
15	GATA2	chr5:177025476-177025942	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr5:177025565-177025918	GM12891	blood:	n/a	n/a
17	POLR2A	chr5:177025467-177025693	A549	lung:	n/a	n/a
18	POLR2A	chr5:177025523-177028484	HepG2	liver:	n/a	n/a
19	POLR2A	chr5:177025437-177025918	U87	brain:	n/a	n/a
20	POLR2A	chr5:177025463-177025795	HL-60	blood:	n/a	n/a
21	POLR2A	chr5:177025345-177025985	GM12891	blood:	n/a	n/a
22	POLR2A	chr5:177025478-177025729	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr5:177025377-177025948	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr5:177025418-177025845	GM12891	blood:	n/a	n/a
25	POLR2A	chr5:177025404-177026411	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:177025419-177026373	GM12878	blood:	n/a	n/a
27	EGR1	chr5:177025521-177025845	K562	blood:	n/a	n/a
28	POLR2A	chr5:177025507-177025686	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:177025411-177025760	GM12891	blood:	n/a	n/a
30	POLR2A	chr5:177025307-177026489	GM12892	blood:	n/a	n/a
31	POLR2A	chr5:177025581-177025625	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:177025404-177028000	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:177025419-177026240	K562	blood:	n/a	n/a
34	POLR2A	chr5:177025382-177026279	K562	blood:	n/a	n/a
35	POLR2A	chr5:177025378-177025982	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr5:177025389-177026366	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:177025246-177026443	HUVEC	blood vessel:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177025539..177028252-chr5:177630597..177632555,2	K562	blood:
2	chr5:176980839..176983786-chr5:177025411..177027346,2	MCF-7	breast:
3	chr5:176895756..176898053-chr5:177023963..177026358,2	K562	blood:
4	chr5:177025398..177027289-chr5:177540105..177542434,2	MCF-7	breast:
5	chr5:177010880..177013120-chr5:177024317..177026904,2	K562	blood:
6	chr5:176942355..176946513-chr5:177025554..177029046,7	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28499092	0.81[EUR][1000 genomes]
rs55646352	0.91[EUR][1000 genomes]
rs55869062	0.97[EUR][1000 genomes]
rs55975666	0.97[EUR][1000 genomes]
rs56190755	0.97[EUR][1000 genomes]
rs56664111	0.97[EUR][1000 genomes]
rs57593509	0.97[EUR][1000 genomes]
rs57960711	0.97[EUR][1000 genomes]
rs59621415	0.97[EUR][1000 genomes]
rs59666704	0.87[EUR][1000 genomes]
rs60634107	0.97[EUR][1000 genomes]
rs61334447	0.97[EUR][1000 genomes]
rs73337744	0.97[EUR][1000 genomes]
rs73337753	0.97[EUR][1000 genomes]
rs73337757	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337765	0.97[EUR][1000 genomes]
rs73337767	0.97[EUR][1000 genomes]
rs73337782	0.97[EUR][1000 genomes]
rs73337783	0.97[EUR][1000 genomes]
rs73337790	0.97[EUR][1000 genomes]
rs73339755	0.97[EUR][1000 genomes]
rs73339759	0.97[EUR][1000 genomes]
rs901380	0.97[EUR][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:119 , 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	chr5:177022200-177025600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:177022400-177026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:177022400-177026200	Weak transcription	Fetal Kidney	kidney
6	chr5:177023000-177025600	Weak transcription	Stomach Mucosa	stomach
7	chr5:177023000-177026000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:177023200-177026200	Weak transcription	Psoas Muscle	Psoas
9	chr5:177023400-177025600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:177023400-177025600	Weak transcription	Hela-S3	cervix
11	chr5:177023400-177026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:177023400-177026200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:177023400-177026200	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:177023600-177025600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:177023600-177025600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:177023600-177026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:177023600-177026200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:177023800-177025600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:177023800-177025600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:177023800-177025600	Weak transcription	Primary B cells from cord blood	blood
21	chr5:177023800-177025600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:177023800-177025600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:177023800-177025600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:177023800-177026000	Weak transcription	Brain Anterior Caudate	brain
25	chr5:177023800-177026200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:177023800-177026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:177023800-177026200	Weak transcription	Brain Angular Gyrus	brain
28	chr5:177023800-177026200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:177023800-177026200	Weak transcription	Brain Substantia Nigra	brain
30	chr5:177023800-177026200	Weak transcription	Pancreas	Pancrea
31	chr5:177023800-177026200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:177023800-177026200	Weak transcription	NHDF-Ad	bronchial
33	chr5:177023800-177026600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:177023800-177026600	Weak transcription	Aorta	Aorta
35	chr5:177023800-177026600	Weak transcription	Gastric	stomach
36	chr5:177023800-177026600	Weak transcription	HSMM	muscle
37	chr5:177023800-177026600	Weak transcription	HSMMtube	muscle
38	chr5:177024000-177025600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:177024000-177025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:177024000-177025600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:177024000-177025600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:177024000-177025600	Weak transcription	Adipose Nuclei	Adipose
43	chr5:177024000-177025600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:177024000-177025600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:177024000-177025600	Weak transcription	Spleen	Spleen
46	chr5:177024000-177025600	Weak transcription	HMEC	breast
47	chr5:177024000-177025600	Weak transcription	NH-A	brain
48	chr5:177024000-177025800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr5:177024000-177025800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:177024000-177025800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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