Variant report

Variant	rs2123459
Chromosome Location	chr14:64952303-64952304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64804683..64806221-chr14:64950769..64952407,2	MCF-7	breast:
2	chr14:64951858..64954186-chr14:64963285..64964978,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140009	Chromatin interaction
ENSG00000214770	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10131416	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10132424	0.85[YRI][hapmap]
rs10132969	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10133243	0.82[YRI][hapmap]
rs10133411	0.84[ASW][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs10133696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10133848	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10134530	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136732	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142879	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10143839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145001	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10145005	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10145013	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10147522	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10150781	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873173	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11158542	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11158543	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11623457	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11625265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11626222	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11627387	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628221	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11845653	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11848179	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11849935	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851236	0.91[EUR][1000 genomes]
rs12050238	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12050358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12385918	0.84[ASW][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs12588886	0.82[YRI][hapmap]
rs1453004	0.84[ASW][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs1453007	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1453009	0.84[ASW][hapmap];0.84[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs1470851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1966865	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1980519	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1980520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1982440	0.87[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs2045024	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198347	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2281603	0.81[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs28469649	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28666045	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28730549	0.92[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28738919	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28766386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28827477	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35115595	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742608	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783722	0.85[YRI][hapmap]
rs3783724	0.85[YRI][hapmap]
rs3783727	0.84[EUR][1000 genomes]
rs4632045	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57525201	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59213791	0.83[AFR][1000 genomes]
rs59577187	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61985663	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61985668	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61985706	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6573559	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7160131	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs7160634	0.89[GIH][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73265639	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73265640	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73265641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs745686	0.87[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs926803	0.87[GIH][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9323450	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs9323451	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9323452	0.94[AMR][1000 genomes];0.99[EUR][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	nsv902022	chr14:64926581-64958638	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2123459	ZBTB25	cis	cerebellum	SCAN
rs2123459	ZBTB1	Cis_1M	lymphoblastoid	RTeQTL
rs2123459	ZBTB1	cis	cerebellum	SCAN
rs2123459	ZBTB25	Cis_1M	lymphoblastoid	RTeQTL
rs2123459	ZBTB25	cis	Nerve Tibial	GTEx
rs2123459	ZBTB25	cis	lymphoblastoid	seeQTL
rs2123459	ZBTB25	cis	multi-tissue	Pritchard
rs2123459	ZBTB25	cis	lung	GTEx
rs2123459	ZBTB25	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64933000-64953400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:64933000-64953600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr14:64933000-64953600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:64933000-64953600	Weak transcription	Lung	lung
5	chr14:64933000-64953600	Weak transcription	Ovary	ovary
6	chr14:64933000-64953600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:64933000-64953600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr14:64933000-64953600	Weak transcription	HSMM	muscle
9	chr14:64933000-64953600	Weak transcription	NHLF	lung
10	chr14:64933200-64953600	Weak transcription	Primary B cells from cord blood	blood
11	chr14:64933200-64953600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr14:64933200-64953600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr14:64933200-64953600	Weak transcription	NHEK	skin
14	chr14:64933200-64953800	Weak transcription	Fetal Brain Female	brain
15	chr14:64933200-64953800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr14:64933200-64968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:64933400-64953600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:64933400-64953600	Weak transcription	Brain Hippocampus Middle	brain
19	chr14:64933400-64953600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:64933400-64953600	Weak transcription	Fetal Stomach	stomach
21	chr14:64933400-64953600	Weak transcription	NH-A	brain
22	chr14:64933400-64968200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr14:64933600-64953600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr14:64934000-64953600	Weak transcription	Thymus	Thymus
25	chr14:64934200-64953800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr14:64934400-64953600	Weak transcription	Adipose Nuclei	Adipose
27	chr14:64935600-64953600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr14:64936800-64968400	Weak transcription	Fetal Brain Male	brain
29	chr14:64939000-64953600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:64940800-64954000	Weak transcription	Colon Smooth Muscle	Colon
31	chr14:64941000-64953600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:64941000-64953800	Weak transcription	Brain Germinal Matrix	brain
33	chr14:64941000-64954000	Weak transcription	Esophagus	oesophagus
34	chr14:64941000-64954000	Weak transcription	Psoas Muscle	Psoas
35	chr14:64942400-64953600	Weak transcription	Fetal Muscle Leg	muscle
36	chr14:64942400-64954000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr14:64942800-64953200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:64942800-64953600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr14:64942800-64953600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr14:64942800-64953600	Weak transcription	Brain Substantia Nigra	brain
41	chr14:64942800-64953800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr14:64942800-64954600	Weak transcription	Fetal Kidney	kidney
43	chr14:64943000-64953800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:64943000-64954000	Weak transcription	HepG2	liver
45	chr14:64943600-64953600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr14:64943600-64954000	Weak transcription	Right Ventricle	heart
47	chr14:64943800-64953600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr14:64944200-64952600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr14:64944200-64953600	Weak transcription	Aorta	Aorta
50	chr14:64944200-64953600	Weak transcription	Brain Cingulate Gyrus	brain

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