Variant report

Variant	rs25655
Chromosome Location	chr1:223900408-223900409
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223900203..223902153-chr1:223927273..223928993,2	K562	blood:
2	chr1:223900140..223900711-chr19:13263508..13264391,2	Hela-S3	cervix:
3	chr1:223899719..223901460-chr1:224517221..224519970,2	K562	blood:
4	chr1:223899985..223900593-chr9:131873619..131874256,2	Hela-S3	cervix:
5	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
6	chr1:223900402..223903093-chr1:223939885..223943104,3	K562	blood:
7	chr1:223900176..223902216-chr1:223970691..223973184,2	MCF-7	breast:
8	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
9	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
10	chr1:223899965..223900475-chr5:77655637..77656578,2	Hela-S3	cervix:
11	chr1:223899719..223902673-chr1:224516675..224518721,2	K562	blood:
12	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
13	chr1:223900092..223902158-chr1:223929992..223931627,2	K562	blood:
14	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
15	chr1:223900203..223901722-chr1:223926667..223928773,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000085365	Chromatin interaction
ENSG00000245556	Chromatin interaction
ENSG00000143748	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction
ENSG00000119383	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10753427	1.00[AMR][1000 genomes]
rs10799364	1.00[AMR][1000 genomes]
rs10915854	1.00[AMR][1000 genomes]
rs10916015	1.00[AMR][1000 genomes]
rs1222144	1.00[AMR][1000 genomes]
rs1361915	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1539703	1.00[AMR][1000 genomes]
rs1539704	1.00[YRI][hapmap]
rs1539706	0.84[AFR][1000 genomes]
rs16842210	1.00[AMR][1000 genomes]
rs16842251	1.00[AMR][1000 genomes]
rs1857549	1.00[AMR][1000 genomes]
rs1892071	1.00[AMR][1000 genomes]
rs1892074	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1892075	1.00[AMR][1000 genomes]
rs1977898	1.00[AMR][1000 genomes]
rs2000317	1.00[AMR][1000 genomes]
rs2096343	1.00[AMR][1000 genomes]
rs2154115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2186005	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2404288	1.00[AMR][1000 genomes]
rs28370086	1.00[AMR][1000 genomes]
rs28370105	1.00[AMR][1000 genomes]
rs28370108	1.00[AMR][1000 genomes]
rs4653792	1.00[AMR][1000 genomes]
rs4653829	0.84[AFR][1000 genomes]
rs4653866	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4653869	1.00[AMR][1000 genomes]
rs6422641	1.00[AMR][1000 genomes]
rs6688648	1.00[AMR][1000 genomes]
rs7538151	1.00[AMR][1000 genomes]
rs7554290	1.00[AMR][1000 genomes]
rs9660081	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	esv3344542	chr1:223899354-223901902	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223899400-223901400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:223899600-223900600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:223899600-223901000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr1:223899600-223901000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:223899600-223901000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:223899600-223901000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:223899600-223901000	Active TSS	Brain Anterior Caudate	brain
8	chr1:223899600-223901000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr1:223899600-223901000	Active TSS	Colon Smooth Muscle	Colon
10	chr1:223899600-223901000	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:223899600-223901200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:223899600-223901200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:223899600-223901200	Active TSS	Brain Germinal Matrix	brain
14	chr1:223899600-223901400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:223899600-223901800	Active TSS	Gastric	stomach
16	chr1:223899600-223901800	Active TSS	HSMMtube	muscle
17	chr1:223899800-223900800	Active TSS	Primary T cells from cord blood	blood
18	chr1:223899800-223900800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:223899800-223900800	Active TSS	Fetal Brain Female	brain
20	chr1:223899800-223900800	Weak transcription	Fetal Heart	heart
21	chr1:223899800-223901000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:223899800-223901000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
23	chr1:223899800-223901000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:223899800-223901000	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:223899800-223901000	Active TSS	Brain Hippocampus Middle	brain
26	chr1:223899800-223901200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:223899800-223901200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:223899800-223901200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:223899800-223901200	Bivalent/Poised TSS	Fetal Thymus	thymus
30	chr1:223899800-223901200	Active TSS	Ovary	ovary
31	chr1:223899800-223901200	Active TSS	Pancreas	Pancrea
32	chr1:223899800-223901200	Bivalent/Poised TSS	Thymus	Thymus
33	chr1:223899800-223901400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:223899800-223901400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:223899800-223901400	Active TSS	Left Ventricle	heart
36	chr1:223899800-223901400	Active TSS	Psoas Muscle	Psoas
37	chr1:223899800-223901400	Bivalent/Poised TSS	HepG2	liver
38	chr1:223899800-223901600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:223899800-223901600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:223899800-223901600	Active TSS	Fetal Kidney	kidney
41	chr1:223899800-223901800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:223899800-223901800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:223899800-223901800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:223899800-223901800	Active TSS	Aorta	Aorta
45	chr1:223899800-223902000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:223899800-223902000	Active TSS	Esophagus	oesophagus
47	chr1:223900000-223900600	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:223900000-223900600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:223900000-223900600	Transcr. at gene 5' and 3'	Right Atrium	heart
50	chr1:223900000-223900800	Active TSS	Primary B cells from peripheral blood	blood

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