Variant report

Variant	rs1658125
Chromosome Location	chr18:28680371-28680372
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:28679636-28682676	K562	blood:	n/a	n/a
2	BHLHE40	chr18:28679783-28680484	K562	blood:	n/a	n/a
3	POLR2A	chr18:28679933-28682875	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr18:28680222-28680516	K562	blood:	n/a	n/a
5	POLR2A	chr18:28680220-28682702	K562	blood:	n/a	n/a
6	POLR2A	chr18:28680128-28680486	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr18:28679911-28682852	HepG2	liver:	n/a	n/a
8	POLR2A	chr18:28680300-28683139	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr18:28680002-28683936	K562	blood:	n/a	n/a
10	REST	chr18:28679865-28682873	H1-neurons	neurons:	n/a	chr18:28682133-28682146
11	KAP1	chr18:28679534-28680579	HEK293	kidney:	n/a	n/a
12	POLR2A	chr18:28680252-28682692	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28678241..28681068-chr18:28692831..28695270,2	K562	blood:
2	chr18:28663717..28665312-chr18:28679601..28681471,2	K562	blood:

Variant related genes	Relation type
ENSG00000265888	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12960042	0.82[AFR][1000 genomes]
rs1437604	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1595358	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1626700	0.86[EUR][1000 genomes]
rs1658111	1.00[CEU][hapmap]
rs1658112	1.00[CEU][hapmap]
rs1658130	0.86[EUR][1000 genomes]
rs1789072	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs1790669	0.86[EUR][1000 genomes]
rs1790670	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1790671	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1790673	0.86[EUR][1000 genomes]
rs1790674	0.85[EUR][1000 genomes]
rs1790675	0.86[EUR][1000 genomes]
rs1790706	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2577079	1.00[CEU][hapmap]
rs4799565	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3384119	chr18:28679654-28682652	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28640800-28680400	Weak transcription	Right Ventricle	heart
2	chr18:28642800-28680600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:28649200-28680800	Weak transcription	Gastric	stomach
4	chr18:28676600-28680400	Weak transcription	Stomach Mucosa	stomach
5	chr18:28678800-28680600	Enhancers	Brain Substantia Nigra	brain
6	chr18:28678800-28682400	Active TSS	Duodenum Mucosa	Duodenum
7	chr18:28679000-28680400	Enhancers	Fetal Heart	heart
8	chr18:28679000-28680400	Flanking Active TSS	K562	blood
9	chr18:28679200-28682800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr18:28679400-28680400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:28679600-28680600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr18:28679800-28680400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr18:28679800-28680400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr18:28679800-28680400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr18:28679800-28680400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr18:28679800-28680400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr18:28679800-28680400	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr18:28679800-28680400	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr18:28679800-28680400	Enhancers	Left Ventricle	heart
20	chr18:28679800-28680400	Flanking Active TSS	Pancreas	Pancrea
21	chr18:28679800-28680400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
22	chr18:28679800-28680400	Flanking Active TSS	HepG2	liver
23	chr18:28679800-28680600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:28679800-28680600	Flanking Active TSS	HMEC	breast
25	chr18:28679800-28680600	Flanking Active TSS	NHEK	skin
26	chr18:28679800-28680800	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr18:28679800-28680800	Bivalent/Poised TSS	Fetal Brain Male	brain
28	chr18:28679800-28681000	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr18:28679800-28681200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr18:28679800-28682400	Active TSS	Esophagus	oesophagus
31	chr18:28679800-28682800	Active TSS	Rectal Smooth Muscle	rectum
32	chr18:28680000-28680400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr18:28680000-28680400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr18:28680000-28680400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:28680000-28680400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:28680000-28680400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
37	chr18:28680000-28680600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:28680000-28680600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr18:28680000-28680600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr18:28680000-28680600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr18:28680000-28680800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
42	chr18:28680000-28680800	Active TSS	Brain Hippocampus Middle	brain
43	chr18:28680000-28682600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr18:28680000-28682600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr18:28680000-28682800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr18:28680000-28682800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr18:28680200-28680400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr18:28680200-28680400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr18:28680200-28680400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr18:28680200-28680400	Flanking Active TSS	Liver	Liver

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