Variant report

Variant	rs12605853
Chromosome Location	chr18:29524251-29524252
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	POLR2A	chr18:29522074-29524311	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:29522017-29524380	HepG2	liver:	n/a	n/a
3	TEAD4	chr18:29522725-29524272	ECC-1	luminal epithelium:	n/a	chr18:29522963-29522972
4	MYC	chr18:29522286-29524727	K562	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
5	TAL1	chr18:29524036-29524730	K562	blood:	n/a	n/a
6	ARID3A	chr18:29524025-29524906	K562	blood:	n/a	n/a
7	CHD1	chr18:29523610-29524255	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr18:29523019-29524380	MCF10A-Er-Src	breast:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
9	CUX1	chr18:29524138-29524424	K562	blood:	n/a	n/a
10	MAX	chr18:29524247-29524468	K562	blood:	n/a	n/a
11	MXI1	chr18:29521978-29525320	SK-N-SH	brain:	n/a	n/a
12	RCOR1	chr18:29524169-29524846	K562	blood:	n/a	n/a
13	ATF1	chr18:29524097-29524682	K562	blood:	n/a	n/a
14	JUN	chr18:29521820-29525062	K562	blood:	n/a	chr18:29524927-29524938 chr18:29524884-29524893 chr18:29523238-29523247 chr18:29523904-29523913 chr18:29523903-29523912 chr18:29524929-29524937
15	MAX	chr18:29522058-29524438	NB4	blood:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
16	MYC	chr18:29522932-29524302	MCF10A-Er-Src	breast:	n/a	chr18:29523105-29523121 chr18:29523114-29523123
17	POLR2A	chr18:29522114-29524302	HL-60	blood:	n/a	n/a
18	IRF1	chr18:29524177-29524640	K562	blood:	n/a	n/a
19	TBL1XR1	chr18:29524144-29524788	K562	blood:	n/a	n/a
20	MAX	chr18:29524198-29524556	K562	blood:	n/a	n/a
21	POLR2A	chr18:29522326-29524897	Raji	blood:	n/a	n/a
22	SIN3A	chr18:29522026-29524605	H1-hESC	embryonic stem cell:	n/a	chr18:29523115-29523124

No.	Distal block	Cell Line	Cell type
1	chr18:29523882..29525586-chr18:29646566..29649385,2	K562	blood:
2	chr18:29522249..29524505-chr18:29596603..29599089,2	MCF-7	breast:
3	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
4	chr17:48942638..48944565-chr18:29522050..29524653,2	MCF-7	breast:
5	chr18:29518719..29521005-chr18:29521192..29525426,5	MCF-7	breast:
6	chr18:29521665..29524441-chr18:29544834..29547590,2	K562	blood:
7	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
8	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
9	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
10	chr18:29468408..29471507-chr18:29523062..29524905,3	K562	blood:
11	chr18:29523716..29526205-chr18:29536614..29539662,3	K562	blood:

Variant related genes	Relation type
TRAPPC8	TF binding region
ENSG00000263917	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000101695	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000266105	Chromatin interaction
ENSG00000141232	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12604916	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604977	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276143	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59301557	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29520200-29526800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:29521000-29524400	Active TSS	Psoas Muscle	Psoas
3	chr18:29521200-29524400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:29521200-29524400	Active TSS	GM12878-XiMat	blood
5	chr18:29521200-29524800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr18:29521200-29524800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr18:29521200-29525200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr18:29521400-29524400	Active TSS	Fetal Kidney	kidney
9	chr18:29521400-29524600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29521400-29524600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr18:29521400-29525000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:29521400-29525400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr18:29521600-29524800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr18:29521600-29524800	Active TSS	HSMMtube	muscle
15	chr18:29521600-29525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr18:29521800-29524400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr18:29521800-29524400	Active TSS	Fetal Muscle Trunk	muscle
18	chr18:29521800-29524600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:29521800-29524600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr18:29522000-29524400	Active TSS	Brain Anterior Caudate	brain
21	chr18:29522000-29524600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:29522000-29524600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr18:29522000-29524800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr18:29522000-29524800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:29522000-29525000	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr18:29522000-29525000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr18:29522000-29525600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr18:29522400-29524400	Active TSS	Rectal Smooth Muscle	rectum
29	chr18:29522600-29524400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr18:29522600-29524400	Active TSS	Fetal Brain Male	brain
31	chr18:29523400-29524400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr18:29523400-29524400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr18:29523400-29524400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr18:29523400-29524400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr18:29523400-29524600	Flanking Active TSS	NH-A	brain
36	chr18:29523400-29524600	Flanking Active TSS	NHEK	skin
37	chr18:29523400-29524800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr18:29523400-29524800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:29523400-29524800	Flanking Active TSS	Dnd41	blood
40	chr18:29523400-29525000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr18:29523600-29524400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr18:29523600-29524400	Active TSS	Brain Germinal Matrix	brain
43	chr18:29523600-29524400	Flanking Active TSS	Fetal Stomach	stomach
44	chr18:29523600-29524400	Active TSS	Right Atrium	heart
45	chr18:29523600-29524600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr18:29523600-29524600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr18:29523600-29524600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr18:29523600-29524800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:29523800-29524400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr18:29523800-29524400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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