Variant report

Variant	rs6105630
Chromosome Location	chr20:16555547-16555548
allele	C/G
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	EBF1	chr20:16555424-16555796	GM12878	blood:	n/a	n/a
3	CTCF	chr20:16555520-16555670	HUVEC	blood vessel:	n/a	chr20:16555525-16555543
4	MAX	chr20:16555327-16556114	H1-hESC	embryonic stem cell:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
5	FOSL2	chr20:16555224-16555884	A549	lung:	n/a	n/a
6	NR3C1	chr20:16555404-16555876	A549	lung:	n/a	chr20:16555690-16555707
7	SIN3AK20	chr20:16555450-16556051	SK-N-SH	brain:	n/a	n/a
8	RCOR1	chr20:16555268-16556030	HepG2	liver:	n/a	n/a
9	MYC	chr20:16555497-16555888	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr20:16554949-16556346	HepG2	liver:	n/a	n/a
11	POLR2A	chr20:16555492-16555930	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr20:16555201-16556115	PANC-1	pancreas:	n/a	n/a
13	MAFF	chr20:16555341-16555980	HepG2	liver:	n/a	n/a
14	YY1	chr20:16555368-16555707	GM12878	blood:	n/a	chr20:16555652-16555663
15	POLR2A	chr20:16555429-16555853	HepG2	liver:	n/a	n/a
16	E2F6	chr20:16555479-16555838	K562	blood:	n/a	n/a
17	RFX5	chr20:16555383-16555712	H1-hESC	embryonic stem cell:	n/a	n/a
18	BHLHE40	chr20:16555255-16555945	K562	blood:	n/a	n/a
19	NR3C1	chr20:16555515-16555783	ECC-1	luminal epithelium:	n/a	chr20:16555690-16555707
20	ZNF143	chr20:16555445-16555771	GM12878	blood:	n/a	n/a
21	MYC	chr20:16555474-16556074	MCF10A-Er-Src	breast:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
22	TAF1	chr20:16555320-16555853	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr20:16555382-16555769	ECC-1	luminal epithelium:	n/a	chr20:16555652-16555663
24	SIN3A	chr20:16555423-16555967	GM12878	blood:	n/a	n/a
25	HCFC1	chr20:16555379-16555886	K562	blood:	n/a	n/a
26	YY1	chr20:16555390-16555712	GM12891	blood:	n/a	chr20:16555652-16555663
27	MYC	chr20:16555335-16555816	H1-hESC	embryonic stem cell:	n/a	n/a
28	KAP1	chr20:16555136-16556386	U2OS	brain:	n/a	n/a
29	MAX	chr20:16555358-16556124	SK-N-SH	brain:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
30	NR3C1	chr20:16555445-16555896	A549	lung:	n/a	chr20:16555690-16555707
31	MAX	chr20:16555303-16556175	K562	blood:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
32	TAF1	chr20:16555413-16555884	HepG2	liver:	n/a	n/a
33	CEBPD	chr20:16555201-16555859	HepG2	liver:	n/a	n/a
34	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
35	SP1	chr20:16555243-16555841	H1-hESC	embryonic stem cell:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
36	TCF7L2	chr20:16555063-16555913	HCT-116	colon:	n/a	n/a
37	EP300	chr20:16555471-16556098	HepG2	liver:	n/a	n/a
38	RUNX3	chr20:16555377-16555716	GM12878	blood:	n/a	n/a
39	EP300	chr20:16555328-16556355	K562	blood:	n/a	n/a
40	SP1	chr20:16555290-16555784	H1-hESC	embryonic stem cell:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
41	SP1	chr20:16555246-16555915	HepG2	liver:	n/a	chr20:16555656-16555668 chr20:16555656-16555668 chr20:16555658-16555667 chr20:16555657-16555666
42	POLR2A	chr20:16555206-16556466	Raji	blood:	n/a	n/a
43	CTCF	chr20:16555520-16555670	HCPEpiC	choroid plexus:	n/a	chr20:16555525-16555543
44	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
45	MAX	chr20:16554937-16556356	A549	lung:	n/a	chr20:16555920-16555927 chr20:16555918-16555928
46	JUND	chr20:16555193-16555854	K562	blood:	n/a	n/a
47	JUND	chr20:16555295-16555878	HepG2	liver:	n/a	n/a
48	JUND	chr20:16555322-16555845	A549	lung:	n/a	n/a
49	TCF12	chr20:16554999-16556182	A549	lung:	n/a	chr20:16555434-16555444
50	POLR2A	chr20:16555055-16556050	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:16555519-16555569	HL-60	blood:	n/a
2	chr20:16555519-16555569	HCT-116	colon:	n/a
3	chr20:16555519-16555569	SK-N-SH_RA	brain:	n/a
4	chr20:16555519-16555569	GM12878	blood:	n/a
5	chr20:16555519-16555569	PANC-1	pancreas:	n/a
6	chr20:16555519-16555569	SKMC	muscle:	n/a
7	chr20:16555519-16555569	Caco-2	colon:	n/a
8	chr20:16555519-16555569	HPAEpiC	pulmonary alveolar:	n/a
9	chr20:16555519-16555569	HMEC	breast:	n/a
10	chr20:16555519-16555569	MCF-7	breast:	n/a
11	chr20:16555519-16555569	T-47D	breast:	n/a
12	chr20:16555519-16555569	HEK293	kidney:	embryo
13	chr20:16555519-16555569	K562	blood:	n/a
14	chr20:16555519-16555569	HepG2	liver:	n/a
15	chr20:16555519-16555569	BJ	skin:	n/a
16	chr20:16555519-16555569	A549	lung:	n/a
17	chr20:16555519-16555569	HCPEpiC	choroid plexus:	n/a
18	chr20:16555519-16555569	AG04449	skin:	fetal
19	chr20:16555519-16555569	ProgFib	skin:	n/a
20	chr20:16555519-16555569	ovcar-3	ovarian:	n/a
21	chr20:16555519-16555569	BE2_C	brain:	n/a
22	chr20:16555519-16555569	IMR90	lung:	fetal
23	chr20:16555519-16555569	NHDF-neo	bronchial:	n/a
24	chr20:16555519-16555569	ECC-1	luminal epithelium:	n/a
25	chr20:16555519-16555569	HIPEpiC	eye:	n/a
26	chr20:16555519-16555569	GM19239	blood:	n/a
27	chr20:16555519-16555569	HAEpiC	amniotic membrane:	n/a
28	chr20:16555519-16555569	NT2-D1	testis:	n/a
29	chr20:16555519-16555569	CMK	blood:	n/a
30	chr20:16555519-16555569	NHBE	bronchial:	n/a
31	chr20:16555519-16555569	SK-N-MC	brain:	n/a
32	chr20:16555519-16555569	AG10803	skin:	n/a
33	chr20:16555519-16555569	PFSK-1	brain:	n/a
34	chr20:16555519-16555569	GM12891	blood:	n/a
35	chr20:16555519-16555569	RPTEC	kidney:	n/a
36	chr20:16555519-16555569	AoSMC	blood vessel:	n/a
37	chr20:16555519-16555569	GM06990	blood:	n/a
38	chr20:16555519-16555569	HCM	heart:	n/a
39	chr20:16555519-16555569	SAEC	small airway:	n/a
40	chr20:16555519-16555569	PrEC	prostate:	n/a
41	chr20:16555519-16555569	NH-A	brain:	n/a
42	chr20:16555519-16555569	H1-hESC	embryonic stem cell:	embryo
43	chr20:16555519-16555569	Hela-S3	cervix:	n/a
44	chr20:16555519-16555569	GM12892	blood:	n/a
45	chr20:16555519-16555569	Hepatocyte	liver:	n/a
46	chr20:16555519-16555569	AG04450	lung:	fetal
47	chr20:16555519-16555569	NB4	blood:	n/a
48	chr20:16555519-16555569	MCF10A-Er-Src	breast:	n/a
49	chr20:16555519-16555569	HEEpiC	esophagus:	n/a
50	chr20:16555519-16555569	SK-N-SH	brain:	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
KIF16B	CpG island

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2235968	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4297956	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4588261	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813227	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6034536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6034537	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6044117	0.80[EUR][1000 genomes]
rs6044120	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6044140	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6044142	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135804	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6105630	C20orf23	Cis_1M	lymphoblastoid	RTeQTL

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	chr20:16553200-16555800	Active TSS	HSMM	muscle
8	chr20:16553200-16556000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr20:16553200-16556200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr20:16553200-16556400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr20:16553200-16556400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr20:16553200-16556600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:16553400-16556200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:16553400-16556400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr20:16553600-16556200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr20:16553600-16556600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr20:16553800-16556000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:16554200-16555600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr20:16554400-16555600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:16554400-16555600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr20:16554600-16555600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr20:16554600-16555600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:16554600-16555600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr20:16554600-16555600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:16554600-16555600	Enhancers	Primary hematopoietic stem cells	blood
26	chr20:16554600-16555600	Enhancers	Gastric	stomach
27	chr20:16554600-16555600	Flanking Active TSS	HepG2	liver
28	chr20:16554600-16555800	Enhancers	Fetal Brain Male	brain
29	chr20:16554600-16555800	Active TSS	Fetal Heart	heart
30	chr20:16554600-16555800	Active TSS	NHEK	skin
31	chr20:16554600-16556200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:16554600-16556200	Active TSS	Aorta	Aorta
33	chr20:16554600-16556400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr20:16554600-16556400	Active TSS	Fetal Kidney	kidney
35	chr20:16554600-16556400	Enhancers	Spleen	Spleen
36	chr20:16554800-16555600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr20:16554800-16555600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr20:16554800-16555800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr20:16554800-16556200	Active TSS	Colon Smooth Muscle	Colon
40	chr20:16555000-16555600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:16555000-16555600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr20:16555000-16555600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr20:16555000-16555600	Flanking Active TSS	Pancreas	Pancrea
44	chr20:16555000-16555600	Flanking Active TSS	GM12878-XiMat	blood
45	chr20:16555000-16556200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr20:16555000-16556200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr20:16555000-16556400	Flanking Active TSS	Liver	Liver
48	chr20:16555000-16556400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr20:16555000-16556400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr20:16555000-16556400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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