Variant report

Variant	rs28656195
Chromosome Location	chr5:179124673-179124674
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179124250-179127985	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:179124222-179127282	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr5:179124589-179129396	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:179124040-179127985	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:179123448-179124704	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr5:179124543-179124985	K562	blood:	n/a	n/a
7	POLR2A	chr5:179124207-179127860	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:179123704-179127859	GM12891	blood:	n/a	n/a
9	POLR2A	chr5:179124246-179124712	GM12878	blood:	n/a	n/a
10	HEY1	chr5:179124235-179124701	K562	blood:	n/a	n/a
11	POLR2A	chr5:179124211-179124674	GM12892	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
2	chr5:179123960..179129281-chr5:179231995..179235216,8	K562	blood:
3	chr5:179101962..179108661-chr5:179122383..179128408,19	MCF-7	breast:
4	chr5:179123960..179129252-chr5:179231413..179236095,7	K562	blood:
5	chr5:179122850..179128148-chr5:179246584..179249342,5	K562	blood:
6	chr5:179047558..179053114-chr5:179123905..179129187,22	K562	blood:
7	chr5:178985235..178987908-chr5:179124412..179127341,2	MCF-7	breast:
8	chr5:179123896..179127851-chr5:179243560..179246560,5	K562	blood:
9	chr5:178976329..178981059-chr5:179123787..179127407,6	K562	blood:
10	chr5:179123572..179126776-chr5:179221240..179224069,3	MCF-7	breast:
11	chr5:178955819..178957353-chr5:179123603..179125281,2	MCF-7	breast:
12	chr5:179124597..179127055-chr5:179246139..179249577,4	MCF-7	breast:
13	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
14	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
15	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
16	chr5:179100989..179111182-chr5:179122076..179128627,19	K562	blood:
17	chr5:179121400..179128828-chr5:179157984..179161377,21	K562	blood:
18	chr5:179123632..179128657-chr5:179156913..179163491,14	MCF-7	breast:
19	chr5:179124533..179126912-chr5:179247842..179250922,3	K562	blood:
20	chr5:179124035..179127505-chr5:179157238..179162405,12	MCF-7	breast:
21	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:
22	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
23	chr5:179123773..179127716-chr5:179220848..179225521,8	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CBY3-2	chr5:179123601-179124700	NONHSAT105616

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000213316	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000221394	Chromatin interaction
ENSG00000127022	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10040357	1.00[EUR][1000 genomes]
rs10058037	1.00[EUR][1000 genomes]
rs11743197	1.00[EUR][1000 genomes]
rs13356823	1.00[EUR][1000 genomes]
rs13358321	1.00[EUR][1000 genomes]
rs17079679	1.00[EUR][1000 genomes]
rs1960428	1.00[EUR][1000 genomes]
rs269459	1.00[EUR][1000 genomes]
rs269460	1.00[EUR][1000 genomes]
rs28391655	0.89[AFR][1000 genomes]
rs4438838	1.00[EUR][1000 genomes]
rs56844432	1.00[EUR][1000 genomes]
rs57104438	1.00[EUR][1000 genomes]
rs58225020	1.00[EUR][1000 genomes]
rs58297257	1.00[EUR][1000 genomes]
rs58311224	1.00[EUR][1000 genomes]
rs58586529	1.00[EUR][1000 genomes]
rs60822577	1.00[EUR][1000 genomes]
rs61330504	1.00[EUR][1000 genomes]
rs6863030	1.00[EUR][1000 genomes]
rs6872508	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449423	1.00[EUR][1000 genomes]
rs7700775	1.00[ASN][1000 genomes]
rs9329087	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:179118400-179125000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:179123200-179124800	Enhancers	Fetal Thymus	thymus
4	chr5:179123200-179125000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:179123200-179125000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:179123200-179125000	Enhancers	Fetal Muscle Trunk	muscle
7	chr5:179123400-179124800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:179123400-179124800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:179123400-179124800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr5:179123400-179125000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:179123400-179125000	Enhancers	Fetal Intestine Small	intestine
12	chr5:179123400-179125000	Enhancers	Spleen	Spleen
13	chr5:179123600-179124800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:179123600-179124800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr5:179123600-179124800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:179123600-179124800	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:179123600-179124800	Enhancers	Fetal Kidney	kidney
18	chr5:179123600-179124800	Flanking Active TSS	GM12878-XiMat	blood
19	chr5:179123600-179125000	Enhancers	Primary B cells from peripheral blood	blood
20	chr5:179123600-179125000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr5:179123600-179125000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr5:179123600-179125000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:179123600-179125000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:179123600-179125000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:179123600-179125000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:179123800-179124800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr5:179123800-179124800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:179123800-179124800	Enhancers	Adipose Nuclei	Adipose
29	chr5:179123800-179124800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr5:179123800-179125000	Enhancers	Brain Cingulate Gyrus	brain
31	chr5:179123800-179125000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr5:179123800-179125000	Enhancers	Colon Smooth Muscle	Colon
33	chr5:179123800-179125000	Enhancers	Fetal Intestine Large	intestine
34	chr5:179123800-179125000	Enhancers	Rectal Smooth Muscle	rectum
35	chr5:179123800-179125000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr5:179123800-179125000	Enhancers	Stomach Mucosa	stomach
37	chr5:179123800-179125200	Flanking Active TSS	Dnd41	blood
38	chr5:179123800-179125400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:179124000-179125000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:179124000-179125000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr5:179124000-179125000	Enhancers	Fetal Brain Male	brain
42	chr5:179124000-179125000	Enhancers	Placenta	Placenta
43	chr5:179124200-179124800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:179124200-179124800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:179124200-179124800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:179124200-179124800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:179124200-179124800	Enhancers	Psoas Muscle	Psoas
48	chr5:179124200-179125000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr5:179124200-179125000	Enhancers	Brain Substantia Nigra	brain
50	chr5:179124200-179125000	Enhancers	Colonic Mucosa	Colon

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