Variant report

Variant	rs6044135
Chromosome Location	chr20:16555386-16555387
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	NRF1	chr20:16555380-16555772	H1-hESC	embryonic stem cell:	n/a	chr20:16555582-16555593 chr20:16555582-16555596 chr20:16555582-16555593
2	MAX	chr20:16555327-16556114	H1-hESC	embryonic stem cell:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
3	FOSL2	chr20:16555224-16555884	A549	lung:	n/a	n/a
4	RCOR1	chr20:16555268-16556030	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:16554949-16556346	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:16555201-16556115	PANC-1	pancreas:	n/a	n/a
7	MAFF	chr20:16555341-16555980	HepG2	liver:	n/a	n/a
8	YY1	chr20:16555368-16555707	GM12878	blood:	n/a	chr20:16555652-16555663
9	RFX5	chr20:16555383-16555712	H1-hESC	embryonic stem cell:	n/a	n/a
10	BHLHE40	chr20:16555255-16555945	K562	blood:	n/a	n/a
11	TAF1	chr20:16555320-16555853	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr20:16555382-16555769	ECC-1	luminal epithelium:	n/a	chr20:16555652-16555663
13	HCFC1	chr20:16555379-16555886	K562	blood:	n/a	n/a
14	MYC	chr20:16555335-16555816	H1-hESC	embryonic stem cell:	n/a	n/a
15	KAP1	chr20:16555136-16556386	U2OS	brain:	n/a	n/a
16	MAX	chr20:16555358-16556124	SK-N-SH	brain:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
17	MAX	chr20:16555303-16556175	K562	blood:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
18	CEBPD	chr20:16555201-16555859	HepG2	liver:	n/a	n/a
19	SRF	chr20:16555341-16556001	ECC-1	luminal epithelium:	n/a	chr20:16555666-16555680 chr20:16555671-16555682 chr20:16555664-16555681 chr20:16555669-16555682 chr20:16555671-16555680 chr20:16555669-16555682 chr20:16555668-16555682 chr20:16555666-16555684 chr20:16555670-16555681 chr20:16555668-16555683
20	SP1	chr20:16555243-16555841	H1-hESC	embryonic stem cell:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
21	TCF7L2	chr20:16555063-16555913	HCT-116	colon:	n/a	n/a
22	RUNX3	chr20:16555377-16555716	GM12878	blood:	n/a	n/a
23	CTCF	chr20:16555360-16555510	HepG2	liver:	n/a	n/a
24	EP300	chr20:16555328-16556355	K562	blood:	n/a	n/a
25	SP1	chr20:16555290-16555784	H1-hESC	embryonic stem cell:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
26	SP1	chr20:16555246-16555915	HepG2	liver:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
27	POLR2A	chr20:16555206-16556466	Raji	blood:	n/a	n/a
28	SRF	chr20:16555296-16555933	ECC-1	luminal epithelium:	n/a	chr20:16555666-16555680 chr20:16555671-16555682 chr20:16555664-16555681 chr20:16555669-16555682 chr20:16555671-16555680 chr20:16555669-16555682 chr20:16555668-16555682 chr20:16555666-16555684 chr20:16555670-16555681 chr20:16555668-16555683
29	MAX	chr20:16554937-16556356	A549	lung:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
30	JUND	chr20:16555193-16555854	K562	blood:	n/a	n/a
31	JUND	chr20:16555295-16555878	HepG2	liver:	n/a	n/a
32	JUND	chr20:16555322-16555845	A549	lung:	n/a	n/a
33	TCF12	chr20:16554999-16556182	A549	lung:	n/a	chr20:16555434-16555444
34	POLR2A	chr20:16555055-16556050	HepG2	liver:	n/a	n/a
35	SP1	chr20:16555261-16555784	K562	blood:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
36	ELF1	chr20:16555111-16555899	HepG2	liver:	n/a	n/a
37	ARID3A	chr20:16555381-16555850	K562	blood:	n/a	n/a
38	ELF1	chr20:16555181-16555729	HepG2	liver:	n/a	n/a
39	ELF1	chr20:16555090-16555659	K562	blood:	n/a	n/a
40	TBP	chr20:16555286-16555772	H1-hESC	embryonic stem cell:	n/a	n/a
41	EP300	chr20:16555365-16555779	SK-N-SH_RA	brain:	n/a	n/a
42	TAF1	chr20:16555363-16555592	SK-N-SH	brain:	n/a	n/a
43	ZNF384	chr20:16555349-16555687	K562	blood:	n/a	n/a
44	MAX	chr20:16555202-16556289	A549	lung:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
45	MAX	chr20:16555370-16556009	K562	blood:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
46	MAZ	chr20:16555192-16555903	HepG2	liver:	n/a	n/a
47	MAX	chr20:16555326-16556147	ECC-1	luminal epithelium:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
48	TAF1	chr20:16555334-16555904	ECC-1	luminal epithelium:	n/a	n/a
49	MAZ	chr20:16555363-16556104	GM12878	blood:	n/a	chr20:16555920-16555927
50	REST	chr20:16555261-16555862	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16554484..16557263-chr20:16559352..16563570,6	K562	blood:
2	chr20:16549901..16551714-chr20:16554248..16557125,2	MCF-7	breast:

Variant related genes	Relation type
KIF16B	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs6034538	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044127	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6044139	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131843	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6131845	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131846	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6135801	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6044135	DSTN	cis	parietal	SCAN
rs6044135	C20orf7	cis	parietal	SCAN
rs6044135	C20orf23	cis	multi-tissue	Pritchard
rs6044135	ZNF133	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16552200-16556600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr20:16552800-16556400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr20:16552800-16556400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr20:16553000-16556400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr20:16553000-16556400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr20:16553000-16557200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr20:16553200-16555400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:16553200-16555800	Active TSS	HSMM	muscle
9	chr20:16553200-16556000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:16553200-16556200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:16553200-16556400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr20:16553200-16556400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr20:16553200-16556600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:16553400-16556200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:16553400-16556400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr20:16553600-16556200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:16553600-16556600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr20:16553800-16556000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:16554000-16555400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr20:16554200-16555600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr20:16554400-16555600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:16554400-16555600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr20:16554600-16555400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr20:16554600-16555400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr20:16554600-16555400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr20:16554600-16555400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr20:16554600-16555400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr20:16554600-16555400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr20:16554600-16555400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:16554600-16555400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:16554600-16555400	Enhancers	Fetal Stomach	stomach
32	chr20:16554600-16555400	Enhancers	Fetal Thymus	thymus
33	chr20:16554600-16555400	Enhancers	Stomach Mucosa	stomach
34	chr20:16554600-16555400	Enhancers	Thymus	Thymus
35	chr20:16554600-16555400	Weak transcription	HSMMtube	muscle
36	chr20:16554600-16555400	Weak transcription	NH-A	brain
37	chr20:16554600-16555600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr20:16554600-16555600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr20:16554600-16555600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:16554600-16555600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr20:16554600-16555600	Enhancers	Primary hematopoietic stem cells	blood
42	chr20:16554600-16555600	Enhancers	Gastric	stomach
43	chr20:16554600-16555600	Flanking Active TSS	HepG2	liver
44	chr20:16554600-16555800	Enhancers	Fetal Brain Male	brain
45	chr20:16554600-16555800	Active TSS	Fetal Heart	heart
46	chr20:16554600-16555800	Active TSS	NHEK	skin
47	chr20:16554600-16556200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr20:16554600-16556200	Active TSS	Aorta	Aorta
49	chr20:16554600-16556400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr20:16554600-16556400	Active TSS	Fetal Kidney	kidney

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