Variant report

Variant	rs10498516
Chromosome Location	chr14:65109326-65109327
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65102703..65104469-chr14:65109001..65111503,2	MCF-7	breast:
2	chr14:65007817..65010307-chr14:65107845..65109704,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10130241	0.88[ASN][1000 genomes]
rs10130755	0.87[ASN][1000 genomes]
rs10132794	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10133861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10134770	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10138611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10140678	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10144661	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10145003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10145101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10145275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10145844	0.93[ASN][1000 genomes]
rs10150987	0.86[ASN][1000 genomes]
rs10151656	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10467818	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11158547	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11158548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158549	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11158550	0.90[AFR][1000 genomes]
rs11158551	0.90[AFR][1000 genomes]
rs11844669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11846008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11846264	0.88[CHB][hapmap];0.88[GIH][hapmap]
rs11848587	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11850291	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12586275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12588437	0.91[ASN][1000 genomes]
rs12588509	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17101956	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1955661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1955662	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1955663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2123458	0.81[ASN][1000 genomes]
rs28714198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28761289	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884269	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56039018	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56396472	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58268586	0.90[AFR][1000 genomes]
rs58273663	0.90[AFR][1000 genomes]
rs61067746	0.90[AFR][1000 genomes]
rs61987035	0.86[ASN][1000 genomes]
rs61987036	0.91[ASN][1000 genomes]
rs61987038	0.82[ASN][1000 genomes]
rs7140482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148864	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7153518	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7160131	0.94[CHB][hapmap]
rs74056339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74056358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74056359	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8006017	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10498516	ZBTB25	cis	cerebellum	SCAN
rs10498516	ZBTB25	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65099400-65111600	Weak transcription	Osteobl	bone
2	chr14:65103000-65109600	Enhancers	Placenta	Placenta
3	chr14:65103400-65111000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr14:65103800-65111400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:65103800-65111600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr14:65103800-65111800	Weak transcription	Fetal Heart	heart
7	chr14:65103800-65112400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr14:65105000-65110400	Weak transcription	HSMM	muscle
9	chr14:65106800-65111600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:65106800-65111600	Weak transcription	NHLF	lung
11	chr14:65106800-65112600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr14:65106800-65112600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:65106800-65115400	Weak transcription	Fetal Intestine Small	intestine
14	chr14:65107000-65111200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:65107000-65111800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:65107000-65112000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:65107000-65112000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:65108000-65111800	Weak transcription	HMEC	breast
19	chr14:65108200-65112000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:65108600-65109400	Enhancers	A549	lung
21	chr14:65108800-65111000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr14:65108800-65111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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