Variant report

Variant	rs12588509
Chromosome Location	chr14:65047272-65047273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65046215..65048699-chr14:65056837..65059085,2	K562	blood:
2	chr14:65017028..65018763-chr14:65046297..65047824,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10130241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10130755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10132033	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10132424	0.84[CEU][hapmap]
rs10132794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10133243	0.82[CEU][hapmap]
rs10133411	0.84[CEU][hapmap];0.91[MKK][hapmap]
rs10133696	0.82[MKK][hapmap]
rs10133861	0.94[ASN][1000 genomes]
rs10134770	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136732	0.81[MKK][hapmap]
rs10138611	0.87[ASN][1000 genomes]
rs10140678	0.92[ASN][1000 genomes]
rs10142835	0.82[CEU][hapmap]
rs10144661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10145003	0.87[ASN][1000 genomes]
rs10145101	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10145275	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10145844	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149286	0.87[CEU][hapmap]
rs10150987	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10151656	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10467818	0.89[ASN][1000 genomes]
rs10498516	0.91[ASN][1000 genomes]
rs11158547	0.88[ASN][1000 genomes]
rs11158548	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11158549	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11625265	0.82[MKK][hapmap]
rs11844669	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11846008	0.87[ASN][1000 genomes]
rs11846264	0.88[CHB][hapmap]
rs11848587	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11849530	0.83[CEU][hapmap]
rs11850291	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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385918	0.84[CEU][hapmap];0.91[MKK][hapmap]
rs12586275	0.87[ASN][1000 genomes]
rs12588437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588886	0.84[CEU][hapmap]
rs1453004	0.84[CEU][hapmap];0.91[MKK][hapmap]
rs1453009	0.84[CEU][hapmap];0.91[MKK][hapmap]
rs1470851	0.82[MKK][hapmap]
rs17101956	0.92[ASN][1000 genomes]
rs1955661	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1955662	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs1955663	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1982440	0.84[ASW][hapmap];0.84[CEU][hapmap];0.91[MKK][hapmap]
rs2123458	0.86[ASN][1000 genomes]
rs2198347	0.82[MKK][hapmap]
rs2281603	0.84[ASW][hapmap];0.84[CEU][hapmap];0.91[MKK][hapmap]
rs28714198	0.87[ASN][1000 genomes]
rs28761289	0.88[ASN][1000 genomes]
rs2884269	0.94[ASN][1000 genomes]
rs3783722	0.84[CEU][hapmap]
rs3783724	0.84[CEU][hapmap]
rs3783726	0.82[CEU][hapmap]
rs56039018	0.94[ASN][1000 genomes]
rs56396472	0.88[ASN][1000 genomes]
rs56690759	0.83[ASN][1000 genomes]
rs61987034	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61987035	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61987036	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61987038	0.87[ASN][1000 genomes]
rs7140482	0.85[ASN][1000 genomes]
rs7148864	1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7153518	0.84[ASN][1000 genomes]
rs7156649	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs7160131	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs74056339	0.92[ASN][1000 genomes]
rs74056358	0.85[ASN][1000 genomes]
rs74056359	0.88[ASN][1000 genomes]
rs8006017	0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12588509	ZBTB25	cis	multi-tissue	Pritchard
rs12588509	ZBTB25	cis	cerebellum	SCAN
rs12588509	MTHFD1	cis	parietal	SCAN
rs12588509	ZBTB1	cis	cerebellum	SCAN
rs12588509	ZBTB25	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65021600-65047600	Weak transcription	Pancreas	Pancrea
2	chr14:65040200-65047400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr14:65040200-65047800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:65040200-65048000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:65040200-65051200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr14:65040200-65058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:65040400-65048000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr14:65041800-65047400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr14:65041800-65048000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr14:65046000-65047400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr14:65046800-65048000	Enhancers	Colon Smooth Muscle	Colon
12	chr14:65046800-65049000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:65047200-65047400	Enhancers	Psoas Muscle	Psoas
14	chr14:65047200-65047800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr14:65047200-65048000	Enhancers	Rectal Smooth Muscle	rectum
16	chr14:65047200-65048200	Enhancers	Fetal Kidney	kidney
17	chr14:65047200-65048600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr14:65047200-65049000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:65047200-65049000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr14:65047200-65049000	Enhancers	HUVEC	blood vessel
21	chr14:65047200-65049200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr14:65047200-65049200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:65047200-65049400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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