Variant report

Variant	rs4144498
Chromosome Location	chr14:68005334-68005335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr14:68005274-68005502	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr14:68005197-68005544	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68003774..68006683-chr14:68064247..68065848,2	MCF-7	breast:
2	chr14:68004052..68005607-chr14:68020967..68023715,2	MCF-7	breast:
3	chr14:67997632..68001958-chr14:68003230..68007409,7	K562	blood:
4	chr14:67997232..68003099-chr14:68003235..68008915,12	K562	blood:
5	chr14:68004825..68008195-chr14:68010390..68013765,5	MCF-7	breast:
6	chr14:67997795..68000777-chr14:68005139..68007037,4	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM229B	TF binding region
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10873205	0.82[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs11158681	0.83[YRI][hapmap]
rs11158684	0.82[YRI][hapmap]
rs12434659	0.81[AFR][1000 genomes]
rs12435433	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2064929	0.84[MEX][hapmap]
rs4902479	0.84[MEX][hapmap];0.86[YRI][hapmap]
rs4902482	0.87[GIH][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap]
rs4902483	0.82[YRI][hapmap]
rs6573780	0.84[MEX][hapmap]
rs7141506	0.82[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs7147529	0.82[GIH][hapmap];0.84[MEX][hapmap];0.93[YRI][hapmap]
rs731681	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs753682	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9671543	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9671816	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9671980	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4144498	RAB15	cis	cerebellum	SCAN
rs4144498	PLEKHH1	cis	cerebellum	SCAN
rs4144498	PLEKHH1	cis	Thyroid	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
2	chr14:68000600-68007000	Weak transcription	Lung	lung
3	chr14:68000800-68005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:68000800-68011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:68000800-68013000	Weak transcription	A549	lung
6	chr14:68001000-68005400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:68001000-68005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:68001000-68007600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr14:68001000-68008000	Weak transcription	K562	blood
10	chr14:68001000-68010600	Weak transcription	Hela-S3	cervix
11	chr14:68001000-68024400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:68001200-68007400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:68001400-68007600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
15	chr14:68001600-68008800	Weak transcription	Fetal Brain Female	brain
16	chr14:68001800-68007000	Weak transcription	Fetal Intestine Large	intestine
17	chr14:68001800-68023600	Weak transcription	HepG2	liver
18	chr14:68002000-68006400	Weak transcription	Fetal Intestine Small	intestine
19	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
20	chr14:68003200-68008200	Weak transcription	Pancreas	Pancrea
21	chr14:68003200-68008400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr14:68003200-68008800	Weak transcription	Placenta	Placenta
23	chr14:68003200-68039800	Weak transcription	Fetal Kidney	kidney
24	chr14:68003400-68005400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:68004000-68006400	Enhancers	Brain Anterior Caudate	brain
26	chr14:68004000-68008200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:68004400-68005400	Enhancers	Primary B cells from peripheral blood	blood
28	chr14:68004400-68005800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:68004400-68005800	Enhancers	HMEC	breast
30	chr14:68004400-68006200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr14:68004600-68005400	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr14:68004600-68005400	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr14:68004600-68005600	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr14:68004600-68005600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr14:68004800-68005400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr14:68004800-68005800	Enhancers	NHEK	skin
37	chr14:68004800-68006000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:68004800-68006400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:68005000-68005400	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr14:68005000-68005400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr14:68005000-68005600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr14:68005000-68005600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr14:68005000-68005600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:68005000-68005600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr14:68005000-68005800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr14:68005000-68006800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr14:68005000-68006800	Enhancers	Adipose Nuclei	Adipose
48	chr14:68005000-68007000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr14:68005200-68005400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr14:68005200-68005600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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