Variant report

Variant	rs10139079
Chromosome Location	chr14:65378042-65378043
allele	A/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	RAD21	chr14:65377441-65378130	SK-N-SH	brain:	n/a	chr14:65377769-65377788
2	CTCF	chr14:65377509-65378151	MCF-7	breast:	n/a	chr14:65377772-65377788 chr14:65377766-65377787
3	RAD21	chr14:65377571-65378102	MCF-7	breast:	n/a	chr14:65377769-65377788
4	RAD21	chr14:65377549-65378046	HCT-116	colon:	n/a	chr14:65377769-65377788
5	RAD21	chr14:65377547-65378101	A549	lung:	n/a	chr14:65377769-65377788
6	CTCF	chr14:65377348-65378173	A549	lung:	n/a	chr14:65377772-65377788 chr14:65377766-65377787
7	CTCF	chr14:65377440-65378165	SK-N-SH	brain:	n/a	chr14:65377772-65377788 chr14:65377766-65377787
8	SMC3	chr14:65377462-65378067	SK-N-SH	brain:	n/a	chr14:65377773-65377787
9	CTCF	chr14:65377960-65378110	GM12878	blood:	n/a	n/a
10	CTCF	chr14:65378040-65378190	RPTEC	kidney:	n/a	n/a
11	CTCF	chr14:65377960-65378110	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr14:65377524-65378108	HCT-116	colon:	n/a	chr14:65377772-65377788 chr14:65377766-65377787

No.	Distal block	Cell Line	Cell type
1	chr14:65290012..65290932-chr14:65377431..65378083,2	MCF-7	breast:
2	chr14:65377652..65378279-chr14:65486390..65487336,2	K562	blood:
3	chr14:65376890..65379070-chr14:65449089..65451973,3	MCF-7	breast:
4	chr14:65376789..65378335-chr14:65383134..65384665,2	MCF-7	breast:
5	chr14:65306477..65308569-chr14:65377752..65379840,2	MCF-7	breast:
6	chr14:65264248..65268196-chr14:65377647..65381035,3	MCF-7	breast:
7	chr14:65263268..65264769-chr14:65377543..65379077,2	K562	blood:
8	chr14:65376372..65378588-chr14:65381042..65383849,2	K562	blood:
9	chr14:65377331..65378166-chr14:65449998..65450968,5	MCF-7	breast:

Variant related genes	Relation type
CHURC1-FNTB	TF binding region
CHURC1	TF binding region
FNTB	TF binding region
RPPH1-2P	TF binding region
ENSG00000258289	Chromatin interaction
ENSG00000125954	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10129479	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10131002	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132396	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10132858	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10133054	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10133290	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10137070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10138534	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139435	0.96[AFR][1000 genomes]
rs10139595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10141986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142016	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142379	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10143017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10144942	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10146885	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10147758	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10148687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10149617	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10151701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12172810	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17102298	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17880380	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17881498	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412065	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28451373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28508270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3949937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899152	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899153	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902332	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902338	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902340	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902345	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902346	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67330703	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7143764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144811	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153503	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8943	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8984	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9281	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693169	chr14:65344400-65381068	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1311	chr14:65352722-65379802	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10139079	CHURC1	cis	Skin Sun Exposed Lower leg	GTEx
rs10139079	CHURC1	cis	Thyroid	GTEx
rs10139079	CHURC1	cis	Nerve Tibial	GTEx
rs10139079	CHURC1	cis	Heart Left Ventricle	GTEx
rs10139079	CHURC1	Cis_1M	lymphoblastoid	RTeQTL
rs10139079	CHURC1	cis	Muscle Skeletal	GTEx
rs10139079	CHURC1	cis	multi-tissue	Pritchard
rs10139079	CHURC1	cis	Artery Aorta	GTEx
rs10139079	CHURC1	cis	lung	GTEx
rs10139079	CHURC1	cis	Whole Blood	GTEx
rs10139079	CHURC1	cis	Artery Tibial	GTEx
rs10139079	CHURC1	cis	Esophagus Muscularis	GTEx
rs10139079	CHURC1	cis	Esophagus Mucosa	GTEx
rs10139079	CHURC1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65373800-65379000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr14:65374000-65379200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:65378000-65378200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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