Variant report

Variant	rs4683300
Chromosome Location	chr3:46934292-46934293
allele	G/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	MXI1	chr3:46933335-46934705	SK-N-SH	brain:	n/a	n/a
2	MAX	chr3:46933569-46934396	H1-hESC	embryonic stem cell:	n/a	chr3:46933825-46933835
3	HA-E2F1	chr3:46933897-46934458	MCF-7	breast:	n/a	n/a
4	ZNF143	chr3:46933938-46934321	GM12878	blood:	n/a	n/a
5	MAX	chr3:46933545-46934303	MCF-7	breast:	n/a	chr3:46933825-46933835
6	MAX	chr3:46933541-46934302	A549	lung:	n/a	chr3:46933825-46933835
7	SIN3A	chr3:46933666-46934496	H1-hESC	embryonic stem cell:	n/a	chr3:46934386-46934397
8	NFIC	chr3:46933642-46934392	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr3:46933503-46934434	H1-hESC	embryonic stem cell:	n/a	chr3:46933825-46933835
10	MAX	chr3:46933457-46934406	ECC-1	luminal epithelium:	n/a	chr3:46933825-46933835
11	POLR2A	chr3:46933849-46934348	A549	lung:	n/a	n/a
12	MYC	chr3:46933636-46934330	NB4	blood:	n/a	chr3:46933825-46933835
13	FOSL1	chr3:46934049-46934391	H1-hESC	embryonic stem cell:	n/a	n/a
14	GTF2F1	chr3:46934188-46934314	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOSL1	chr3:46933992-46934429	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr3:46933941-46934336	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr3:46933891-46934430	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP1	chr3:46933853-46934387	H1-hESC	embryonic stem cell:	n/a	chr3:46934129-46934140 chr3:46934148-46934159 chr3:46934340-46934353
19	RAD21	chr3:46933786-46934340	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr3:46933464-46934396	A549	lung:	n/a	chr3:46933825-46933835
21	E2F6	chr3:46933682-46934340	A549	lung:	n/a	n/a
22	E2F6	chr3:46933611-46934422	H1-hESC	embryonic stem cell:	n/a	n/a
23	GABPA	chr3:46933951-46934372	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr3:46933588-46934399	ECC-1	luminal epithelium:	n/a	n/a
25	MXI1	chr3:46933364-46934350	IMR90	lung:	n/a	n/a
26	NRF1	chr3:46933758-46934446	SK-N-SH	brain:	n/a	n/a
27	E2F6	chr3:46933521-46934787	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr3:46933535-46934355	ECC-1	luminal epithelium:	n/a	chr3:46933825-46933835
29	POLR2A	chr3:46931669-46936032	K562	blood:	n/a	n/a
30	MAX	chr3:46933643-46934297	NB4	blood:	n/a	chr3:46933825-46933835
31	TBP	chr3:46933895-46934366	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46927679..46930570-chr3:46933189..46935656,3	MCF-7	breast:
2	chr3:46923291..46931131-chr3:46931662..46935716,9	K562	blood:
3	chr3:46929163..46931629-chr3:46932279..46935009,2	K562	blood:
4	chr3:46733775..46736386-chr3:46933231..46935509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268537	TF binding region
ENSG00000268537	Chromatin interaction
ENSG00000160808	Chromatin interaction
ENSG00000160801	Chromatin interaction
ENSG00000178038	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1001284	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865943	0.92[ASN][1000 genomes]
rs1138518	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705936	0.92[ASN][1000 genomes]
rs11719795	0.94[ASN][1000 genomes]
rs1466275	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242116	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290545	0.83[ASN][1000 genomes]
rs2290546	0.92[ASN][1000 genomes]
rs4539969	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4587	0.92[ASN][1000 genomes]
rs4682845	0.93[ASN][1000 genomes]
rs4683296	0.91[ASN][1000 genomes]
rs4683297	0.91[ASN][1000 genomes]
rs4683298	0.93[ASN][1000 genomes]
rs4683299	0.90[ASN][1000 genomes]
rs4683301	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442038	0.83[ASN][1000 genomes]
rs6442039	0.83[ASN][1000 genomes]
rs6442040	0.91[ASN][1000 genomes]
rs6780601	0.92[ASN][1000 genomes]
rs724448	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724449	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724450	0.96[ASN][1000 genomes]
rs7623898	0.91[ASN][1000 genomes]
rs7635480	0.85[ASN][1000 genomes]
rs7645278	0.91[ASN][1000 genomes]
rs7646906	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9852082	0.91[ASN][1000 genomes]
rs9855938	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683300	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46933000-46934800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:46933200-46934400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:46933200-46934400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr3:46933400-46934400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:46933400-46934400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:46933400-46934400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr3:46933400-46934400	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr3:46933400-46934400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
9	chr3:46933400-46934600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:46933400-46934600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:46933400-46934600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:46933400-46934600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr3:46933400-46934600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:46933400-46935000	Flanking Active TSS	Fetal Heart	heart
15	chr3:46933600-46934400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:46933600-46934400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:46933600-46934400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:46933600-46934400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:46933600-46934400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr3:46933600-46934400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:46933600-46934400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:46933600-46934400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:46933600-46934400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:46933600-46934400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr3:46933600-46934400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
26	chr3:46933600-46934400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:46933600-46934400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr3:46933600-46934400	Flanking Active TSS	Left Ventricle	heart
29	chr3:46933600-46934400	Flanking Active TSS	Ovary	ovary
30	chr3:46933600-46934400	Flanking Active TSS	Right Ventricle	heart
31	chr3:46933600-46934400	Flanking Active TSS	HUVEC	blood vessel
32	chr3:46933600-46934400	Bivalent/Poised TSS	Osteobl	bone
33	chr3:46933600-46934600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:46933600-46934600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr3:46933600-46934600	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:46933600-46934600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:46933600-46934600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:46933600-46934600	Active TSS	Hela-S3	cervix
39	chr3:46933600-46934800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:46933600-46934800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr3:46933600-46934800	Flanking Active TSS	HSMM	muscle
42	chr3:46933800-46934400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr3:46933800-46934400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:46933800-46934400	Active TSS	Brain Substantia Nigra	brain
45	chr3:46933800-46934400	Flanking Active TSS	Right Atrium	heart
46	chr3:46933800-46934400	Flanking Bivalent TSS/Enh	Dnd41	blood
47	chr3:46933800-46934600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:46933800-46934600	Active TSS	Brain Angular Gyrus	brain
49	chr3:46933800-46934600	Active TSS	Brain Cingulate Gyrus	brain
50	chr3:46933800-46934600	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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