Variant report

Variant	rs1006038
Chromosome Location	chr14:78263321-78263322
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	ZMIZ1	chr14:78263224-78263330	K562	blood:	n/a	n/a

Variant related genes	Relation type
ADCK1	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1006039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1006040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136053	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10139492	0.90[CHB][hapmap]
rs10142722	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10143294	0.90[CHB][hapmap]
rs10144448	0.90[CHB][hapmap]
rs10148373	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10149619	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1048147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10483885	0.90[CHB][hapmap]
rs11159288	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs114763	0.90[CHB][hapmap]
rs11622565	0.83[ASN][1000 genomes]
rs11623088	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624101	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11628888	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs11847025	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12435761	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883228	0.86[ASN][1000 genomes]
rs12885306	0.90[CHB][hapmap]
rs12887282	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12887606	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12890375	0.89[ASN][1000 genomes]
rs12890728	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs13379065	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469018	0.89[ASN][1000 genomes]
rs1477259	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477260	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477261	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1477262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477264	0.90[CHB][hapmap]
rs1549119	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17106157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176941	0.90[CHB][hapmap]
rs176943	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176944	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176952	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176953	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs176955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176956	0.90[CHB][hapmap]
rs176957	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176959	0.90[CHB][hapmap]
rs176960	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs176962	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176963	0.90[CHB][hapmap]
rs176964	1.00[CHB][hapmap]
rs176965	0.90[CHB][hapmap]
rs176966	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176971	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176973	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs176979	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs176980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978416	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984925	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032781	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052444	0.81[MEX][hapmap]
rs2112136	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267756	0.90[CHB][hapmap]
rs2267758	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267760	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2267761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267762	0.90[CHB][hapmap]
rs2267763	0.90[CHB][hapmap]
rs2267764	0.90[CHB][hapmap]
rs2267767	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2267768	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277917	0.90[CHB][hapmap]
rs2284234	0.90[CHB][hapmap]
rs2284235	0.90[CHB][hapmap]
rs2299930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2364584	0.84[ASN][1000 genomes]
rs2364840	0.87[ASN][1000 genomes]
rs2544567	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28534379	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28603114	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35204328	0.83[ASN][1000 genomes]
rs3759728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783983	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4383070	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4632066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4635269	0.82[ASN][1000 genomes]
rs4899670	0.90[CHB][hapmap]
rs4899673	0.90[CHB][hapmap]
rs4903643	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909252	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56017708	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56412551	0.85[ASN][1000 genomes]
rs57635466	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59848135	0.82[AMR][1000 genomes]
rs61993668	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6574388	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6574391	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6574399	0.90[CHB][hapmap]
rs6574402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574404	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7142390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7143926	0.90[CHB][hapmap]
rs7146020	0.81[MEX][hapmap]
rs7147516	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7148078	0.86[CHB][hapmap]
rs7151211	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7151685	0.90[CHB][hapmap]
rs717683	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685264	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs759713	0.90[CHB][hapmap]
rs759808	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8003979	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8011337	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8014635	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015645	0.90[CHB][hapmap]
rs8016175	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8016447	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8018741	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8018971	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323649	0.90[CHB][hapmap]
rs9323650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs9323651	0.90[CHB][hapmap]

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	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2754594	chr14:78222798-78275549	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006038	POMT2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78253800-78266200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:78259600-78266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr14:78261800-78263800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr14:78261800-78264600	Enhancers	Hela-S3	cervix
5	chr14:78262000-78263400	Enhancers	Placenta	Placenta
6	chr14:78262000-78263400	Enhancers	GM12878-XiMat	blood
7	chr14:78262000-78264000	Enhancers	HepG2	liver
8	chr14:78262200-78265800	Weak transcription	K562	blood
9	chr14:78262200-78266000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr14:78262200-78266000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr14:78262400-78265800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:78262400-78266000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:78262400-78266000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr14:78262400-78266000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr14:78262400-78266000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr14:78262400-78266000	Weak transcription	NH-A	brain
17	chr14:78262400-78266200	Weak transcription	HMEC	breast
18	chr14:78262400-78266200	Weak transcription	NHDF-Ad	bronchial
19	chr14:78262600-78265800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr14:78262600-78266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:78262600-78266000	Weak transcription	Osteobl	bone
22	chr14:78262600-78266200	Weak transcription	NHLF	lung
23	chr14:78263000-78265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:78263000-78266000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:78263000-78266000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr14:78263000-78266000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr14:78263000-78266000	Weak transcription	Adipose Nuclei	Adipose
28	chr14:78263000-78266000	Weak transcription	A549	lung
29	chr14:78263000-78266000	Weak transcription	NHEK	skin
30	chr14:78263000-78266200	Weak transcription	Stomach Mucosa	stomach
31	chr14:78263000-78266200	Weak transcription	HSMMtube	muscle
32	chr14:78263200-78266200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:78263200-78266200	Weak transcription	Psoas Muscle	Psoas

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