Variant report

Variant	rs2066276
Chromosome Location	chr10:93557619-93557620
allele	A/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	YY1	chr10:93557567-93558644	SK-N-SH	brain:	n/a	chr10:93558228-93558242 chr10:93558245-93558256 chr10:93558427-93558441 chr10:93558233-93558244 chr10:93558236-93558245 chr10:93558281-93558295 chr10:93558189-93558198 chr10:93558432-93558441
2	MAX	chr10:93557595-93558789	K562	blood:	n/a	chr10:93558281-93558290
3	ZBTB7A	chr10:93557574-93559010	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr10:93557594-93558464	U87	brain:	n/a	n/a
5	MXI1	chr10:93557289-93559806	IMR90	lung:	n/a	n/a
6	RFX5	chr10:93557593-93557933	K562	blood:	n/a	n/a
7	EP300	chr10:93557342-93559350	ECC-1	luminal epithelium:	n/a	chr10:93558379-93558395 chr10:93558934-93558941 chr10:93558236-93558252
8	YY1	chr10:93557532-93558507	SK-N-SH_RA	brain:	n/a	chr10:93558228-93558242 chr10:93558245-93558256 chr10:93558427-93558441 chr10:93558233-93558244 chr10:93558236-93558245 chr10:93558281-93558295 chr10:93558189-93558198 chr10:93558432-93558441
9	POLR2A	chr10:93557479-93559292	HUVEC	blood vessel:	n/a	n/a
10	MXI1	chr10:93557578-93559858	SK-N-SH	brain:	n/a	n/a
11	PML	chr10:93557588-93558545	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:93557476-93559630	Hela-S3	cervix:	n/a	n/a
13	MAZ	chr10:93557505-93558449	GM12878	blood:	n/a	chr10:93558281-93558290
14	POLR2A	chr10:93557591-93559230	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr10:93557532-93559359	NB4	blood:	n/a	chr10:93558281-93558290
16	RFX5	chr10:93557431-93559378	Hela-S3	cervix:	n/a	chr10:93558862-93558875 chr10:93558102-93558117
17	MAX	chr10:93557601-93558456	A549	lung:	n/a	chr10:93558281-93558290
18	POLR2A	chr10:93557593-93558616	HUVEC	blood vessel:	n/a	n/a
19	YY1	chr10:93557573-93558363	A549	lung:	n/a	chr10:93558228-93558242 chr10:93558245-93558256 chr10:93558233-93558244 chr10:93558236-93558245 chr10:93558281-93558295 chr10:93558189-93558198
20	POLR2A	chr10:93557568-93558685	Hela-S3	cervix:	n/a	n/a
21	TCF12	chr10:93557486-93558472	A549	lung:	n/a	n/a
22	SIN3A	chr10:93557498-93559615	H1-hESC	embryonic stem cell:	n/a	chr10:93558411-93558420
23	MYC	chr10:93557612-93558816	K562	blood:	n/a	chr10:93558281-93558290
24	MAX	chr10:93557551-93558756	A549	lung:	n/a	chr10:93558281-93558290
25	USF2	chr10:93557538-93558326	Hela-S3	cervix:	n/a	chr10:93558132-93558145 chr10:93558134-93558143 chr10:93558134-93558143 chr10:93558133-93558142
26	POLR2A	chr10:93557579-93558807	HepG2	liver:	n/a	n/a
27	TBP	chr10:93557372-93558234	Hela-S3	cervix:	n/a	n/a
28	KAP1	chr10:93557605-93558401	HEK293	kidney:	n/a	n/a
29	POLR2A	chr10:93556830-93559405	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr10:93557202-93559639	GM12891	blood:	n/a	n/a
31	POLR2A	chr10:93557594-93558470	U87	brain:	n/a	n/a
32	TAF1	chr10:93557531-93558882	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr10:93557567-93558898	MCF-7	breast:	n/a	n/a
34	REST	chr10:93557454-93559051	H1-neurons	neurons:	n/a	chr10:93558723-93558736 chr10:93558408-93558428 chr10:93558666-93558679
35	CHD1	chr10:93557391-93558364	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr10:93557318-93559614	NB4	blood:	n/a	chr10:93558281-93558290
37	POLR2A	chr10:93557481-93559704	MCF10A-Er-Src	breast:	n/a	n/a
38	YY1	chr10:93557494-93558461	SK-N-SH	brain:	n/a	chr10:93558228-93558242 chr10:93558245-93558256 chr10:93558427-93558441 chr10:93558233-93558244 chr10:93558236-93558245 chr10:93558281-93558295 chr10:93558189-93558198 chr10:93558432-93558441
39	MAX	chr10:93557421-93559346	ECC-1	luminal epithelium:	n/a	chr10:93558281-93558290
40	TAF1	chr10:93557606-93558373	PFSK-1	brain:	n/a	n/a
41	TBL1XR1	chr10:93557619-93558388	GM12878	blood:	n/a	n/a
42	POLR2A	chr10:93557235-93559315	Raji	blood:	n/a	n/a
43	CHD1	chr10:93556973-93559802	IMR90	lung:	n/a	n/a
44	POLR2A	chr10:93557536-93558929	GM12878	blood:	n/a	n/a
45	POLR2A	chr10:93557556-93558514	PFSK-1	brain:	n/a	n/a
46	TAF1	chr10:93557612-93558503	ECC-1	luminal epithelium:	n/a	n/a
47	TAF1	chr10:93557603-93558310	A549	lung:	n/a	n/a
48	NFIC	chr10:93557477-93559042	ECC-1	luminal epithelium:	n/a	n/a
49	NRF1	chr10:93557557-93558611	GM12878	blood:	n/a	chr10:93558115-93558129 chr10:93558115-93558124 chr10:93558112-93558126 chr10:93558115-93558126 chr10:93558114-93558125
50	E2F6	chr10:93557573-93558359	A549	lung:	n/a	chr10:93558116-93558125

No.	Distal block	Cell Line	Cell type
1	chr10:93525967..93528056-chr10:93556170..93559024,2	MCF-7	breast:
2	chr10:93555222..93557965-chr10:93666465..93668632,2	MCF-7	breast:
3	chr10:93556770..93559224-chr10:93566498..93569343,3	MCF-7	breast:
4	chr10:93168839..93171584-chr10:93557037..93559095,2	K562	blood:
5	chr10:93525891..93528491-chr10:93557186..93559232,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFBP3-1	chr10:93557570-93557953	XLOC_008905
2	lnc-FGFBP3-1	chr10:93557570-93557953	NR_108070

Variant related genes	Relation type
TNKS2	TF binding region
ENSG00000272817	Chromatin interaction
ENSG00000165338	Chromatin interaction
ENSG00000180581	Chromatin interaction
ENSG00000228759	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10736064	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10748568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748569	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786011	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10786013	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10786015	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10786018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881934	1.00[JPT][hapmap]
rs10881959	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10881968	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11186695	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186731	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11814405	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12248932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12573311	0.84[ASN][1000 genomes]
rs1340420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1539041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1572933	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1572934	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1770467	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770472	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1770475	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1772180	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1772185	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1935030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935031	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2259280	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2487513	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2487514	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2994394	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3930831	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4403720	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4933677	0.87[GIH][hapmap]
rs6583787	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7073486	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7077236	0.89[EUR][1000 genomes]
rs7085519	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7897784	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7911346	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918126	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs946896	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431124	chr10:93557397-93559945	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2066276	TNKS2-AS1	cis	lung	GTEx
rs2066276	TNKS2-AS1	cis	Thyroid	GTEx
rs2066276	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs2066276	TNKS2-AS1	cis	Artery Aorta	GTEx
rs2066276	TNKS2-AS1	cis	Nerve Tibial	GTEx
rs2066276	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2066276	TNKS2-AS1	cis	Artery Tibial	GTEx
rs2066276	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs2066276	TNKS2-AS1	cis	Stomach	GTEx
rs2066276	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs2066276	TNKS2-AS1	cis	Esophagus Muscularis	GTEx
rs2066276	PPP1R3C	cis	Esophagus Mucosa	GTEx
rs2066276	TNKS2-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93555800-93558000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr10:93555800-93558000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:93556000-93558000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr10:93556000-93558000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr10:93556000-93560000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:93556000-93560000	Active TSS	Aorta	Aorta
7	chr10:93556000-93560000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:93556000-93560200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:93556000-93560200	Active TSS	Stomach Smooth Muscle	stomach
10	chr10:93556000-93560800	Active TSS	Right Atrium	heart
11	chr10:93556000-93561200	Active TSS	Ovary	ovary
12	chr10:93556200-93557800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr10:93556200-93557800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr10:93556200-93557800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr10:93556200-93557800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr10:93556200-93557800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr10:93556200-93557800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr10:93556200-93557800	Flanking Active TSS	NHEK	skin
19	chr10:93556200-93558000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:93556200-93558000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr10:93556200-93558000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr10:93556200-93558000	Flanking Active TSS	HMEC	breast
23	chr10:93556200-93559800	Active TSS	Fetal Stomach	stomach
24	chr10:93556200-93560000	Active TSS	Colonic Mucosa	Colon
25	chr10:93556200-93560200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:93556200-93560200	Active TSS	Right Ventricle	heart
27	chr10:93556200-93560800	Active TSS	Psoas Muscle	Psoas
28	chr10:93556200-93562000	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr10:93556400-93557800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:93556400-93558000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr10:93556400-93558000	Flanking Active TSS	HUVEC	blood vessel
32	chr10:93556400-93559800	Active TSS	Primary T cells fromperipheralblood	blood
33	chr10:93556600-93557800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr10:93556600-93557800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr10:93556600-93557800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr10:93556600-93557800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr10:93556600-93558000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr10:93556600-93560200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr10:93556600-93560400	Active TSS	Fetal Muscle Trunk	muscle
40	chr10:93556800-93557800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:93556800-93557800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:93556800-93557800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:93556800-93557800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr10:93556800-93557800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:93556800-93557800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr10:93556800-93557800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:93556800-93557800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:93556800-93557800	Flanking Active TSS	NHLF	lung
49	chr10:93556800-93558000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:93556800-93558000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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