Variant report

Variant	rs7230885
Chromosome Location	chr18:29598010-29598011
allele	C/T
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	TCF7L2	chr18:29597909-29599544	Hela-S3	cervix:	n/a	n/a
2	EGR1	chr18:29597815-29599185	HCT-116	colon:	n/a	chr18:29598578-29598589 chr18:29598583-29598596 chr18:29599012-29599022 chr18:29598577-29598590 chr18:29598580-29598594
3	SETDB1	chr18:29597909-29598747	U2OS	brain:	n/a	n/a
4	KAP1	chr18:29597881-29600018	HEK293	kidney:	n/a	n/a
5	MAX	chr18:29597849-29600053	HCT-116	colon:	n/a	chr18:29599482-29599489 chr18:29599479-29599490
6	GTF3C2	chr18:29597795-29598495	Hela-S3	cervix:	n/a	n/a
7	MAX	chr18:29597832-29599870	HCT-116	colon:	n/a	chr18:29599482-29599489 chr18:29599479-29599490
8	ZKSCAN1	chr18:29597943-29599029	Hela-S3	cervix:	n/a	n/a
9	TCF7L2	chr18:29597961-29599122	HCT-116	colon:	n/a	n/a
10	KAP1	chr18:29597862-29598983	U2OS	brain:	n/a	n/a
11	HEY1	chr18:29597987-29598981	HepG2	liver:	n/a	chr18:29598626-29598641
12	CTBP2	chr18:29597969-29599684	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29597506..29599866-chr18:29670953..29673378,4	MCF-7	breast:
2	chr18:29596689..29599956-chr18:29670764..29674475,6	MCF-7	breast:
3	chr18:29522249..29524505-chr18:29596603..29599089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263917	TF binding region
RNF125	TF binding region
ENSG00000153339	Chromatin interaction
ENSG00000238982	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000263823	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12455890	0.80[ASN][1000 genomes]
rs12458564	0.80[ASN][1000 genomes]
rs4799322	0.84[EUR][1000 genomes]
rs4799323	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66467030	0.86[EUR][1000 genomes]

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	nsv1065285	chr18:29527884-29614986	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv524199	chr18:29595164-29598809	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29588600-29598200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29593600-29598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:29596400-29598200	Weak transcription	Colon Smooth Muscle	Colon
4	chr18:29597400-29600400	Flanking Active TSS	Dnd41	blood
5	chr18:29597600-29598600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr18:29597600-29599800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:29597600-29600600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:29597800-29598200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr18:29597800-29598200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:29597800-29598200	Active TSS	Duodenum Mucosa	Duodenum
11	chr18:29597800-29598200	Enhancers	Small Intestine	intestine
12	chr18:29597800-29598200	Enhancers	Stomach Mucosa	stomach
13	chr18:29597800-29598400	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr18:29597800-29598400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr18:29597800-29598400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr18:29597800-29598400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr18:29597800-29598400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr18:29597800-29598600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr18:29597800-29598600	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr18:29597800-29598600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr18:29597800-29598600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr18:29597800-29598600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr18:29597800-29598600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr18:29597800-29598600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr18:29597800-29599000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr18:29597800-29599000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr18:29597800-29599400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr18:29597800-29599400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr18:29597800-29599600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr18:29597800-29600000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr18:29597800-29600000	Active TSS	H9 Cell Line	embryonic stem cell
32	chr18:29597800-29600000	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr18:29597800-29600400	Active TSS	Rectal Smooth Muscle	rectum
34	chr18:29597800-29600600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr18:29597800-29600600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr18:29597800-29600800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr18:29597800-29601000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr18:29598000-29598200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:29598000-29598200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr18:29598000-29598200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr18:29598000-29598200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:29598000-29598200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr18:29598000-29598200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr18:29598000-29598200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr18:29598000-29598200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr18:29598000-29598200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:29598000-29598200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
48	chr18:29598000-29598200	Active TSS	Brain Hippocampus Middle	brain
49	chr18:29598000-29598200	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr18:29598000-29598200	Enhancers	Pancreas	Pancrea

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