Variant report

Variant	rs7253056
Chromosome Location	chr19:42978837-42978838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10084159	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10401271	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402361	0.84[AMR][1000 genomes]
rs10402677	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10403517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405646	0.87[AMR][1000 genomes]
rs10405906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407576	0.88[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes]
rs10412463	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10413413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415564	0.80[AMR][1000 genomes]
rs10416089	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10417418	0.80[AMR][1000 genomes]
rs10417693	0.80[AMR][1000 genomes]
rs10419378	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10420796	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10421108	0.86[AMR][1000 genomes]
rs10422987	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10469271	0.87[AMR][1000 genomes]
rs10469284	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs1076243	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083659	0.86[AMR][1000 genomes]
rs11665870	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11665935	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666835	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11666862	0.87[AMR][1000 genomes]
rs11668599	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671272	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671846	1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11673645	1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11879306	0.88[EUR][1000 genomes]
rs11881517	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11882150	0.88[EUR][1000 genomes]
rs12611218	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343936	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975890	0.83[EUR][1000 genomes]
rs1859341	0.80[AMR][1000 genomes]
rs2267631	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs28411988	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28447294	0.80[AMR][1000 genomes]
rs4080606	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499340	0.80[AMR][1000 genomes]
rs55850134	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60313903	0.85[EUR][1000 genomes]
rs6509016	0.84[AFR][1000 genomes]
rs7248297	0.86[AMR][1000 genomes]
rs7253209	0.86[AMR][1000 genomes]
rs8102439	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];0.99[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102519	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103285	0.94[ASW][hapmap];0.88[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103891	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106083	0.80[AMR][1000 genomes]
rs8106570	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107152	0.88[ASW][hapmap];0.88[CEU][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107790	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108844	0.89[YRI][hapmap]
rs8112156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851298	0.85[EUR][1000 genomes]
rs851301	0.88[EUR][1000 genomes]
rs851302	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9304604	0.82[ASW][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.84[AMR][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	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7253056	KCNA7	cis	cerebellum	SCAN
rs7253056	SEC1	cis	cerebellum	SCAN
rs7253056	KLK8	cis	parietal	SCAN
rs7253056	ZNF223	cis	parietal	SCAN
rs7253056	FTL	cis	cerebellum	SCAN
rs7253056	PTOV1	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42971600-42979000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:42972600-42979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:42973800-42981400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr19:42974200-42980200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:42974400-42984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:42974600-42979000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:42974600-42980200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:42975000-42979000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr19:42975000-42981200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr19:42975000-42981400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr19:42975200-42980400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr19:42975400-42979000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr19:42975600-42981600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr19:42976400-42981000	Weak transcription	Adipose Nuclei	Adipose
15	chr19:42977400-42979000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:42977400-42979000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:42977400-42980200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:42977400-42984800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:42977800-42979400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:42978000-42979200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:42978000-42979400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:42978000-42979800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:42978000-42981200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr19:42978200-42980400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:42978400-42981200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:42978800-42979200	Active TSS	Brain Anterior Caudate	brain
27	chr19:42978800-42979400	Active TSS	Brain Hippocampus Middle	brain
28	chr19:42978800-42979800	Enhancers	Brain Cingulate Gyrus	brain

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