Variant report

Variant	rs12333974
Chromosome Location	chr7:69367000-69367001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1014417	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10245786	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10257549	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10259748	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1035013	0.82[ASN][1000 genomes]
rs10452738	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11508453	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761141	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11763186	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11974201	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11978431	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12698813	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698816	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698822	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12698825	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698830	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13226538	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13237811	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140933	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140980	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17140982	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860488	0.84[ASN][1000 genomes]
rs210591	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs210593	0.90[ASN][1000 genomes]
rs210594	0.85[ASN][1000 genomes]
rs210596	0.90[ASN][1000 genomes]
rs210601	0.90[ASN][1000 genomes]
rs210604	0.90[ASN][1000 genomes]
rs210606	0.88[ASN][1000 genomes]
rs2533427	0.82[ASN][1000 genomes]
rs2533428	0.82[ASN][1000 genomes]
rs2533429	0.82[ASN][1000 genomes]
rs2533430	0.84[ASN][1000 genomes]
rs2533431	0.84[ASN][1000 genomes]
rs2533433	0.84[ASN][1000 genomes]
rs2533449	0.84[ASN][1000 genomes]
rs2533458	0.84[ASN][1000 genomes]
rs2851483	0.82[ASN][1000 genomes]
rs2851484	0.82[ASN][1000 genomes]
rs2851487	0.84[ASN][1000 genomes]
rs2851514	0.84[ASN][1000 genomes]
rs2851515	0.82[ASN][1000 genomes]
rs2851516	0.82[ASN][1000 genomes]
rs2865805	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28770244	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34221396	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34617709	0.89[EUR][1000 genomes]
rs35696945	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4717520	0.89[ASN][1000 genomes]
rs4718906	0.84[ASN][1000 genomes]
rs505949	0.84[ASN][1000 genomes]
rs513150	0.85[ASN][1000 genomes]
rs532820	0.86[ASN][1000 genomes]
rs547630	0.84[ASN][1000 genomes]
rs55990156	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs565505	0.84[ASN][1000 genomes]
rs576193	0.84[ASN][1000 genomes]
rs576293	0.87[ASN][1000 genomes]
rs585282	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs589983	0.86[ASN][1000 genomes]
rs590609	0.87[ASN][1000 genomes]
rs593063	0.87[ASN][1000 genomes]
rs595681	0.94[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs60359704	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs610930	0.94[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs626767	0.84[ASN][1000 genomes]
rs627981	0.84[ASN][1000 genomes]
rs6415223	0.83[ASN][1000 genomes]
rs645245	0.84[ASN][1000 genomes]
rs6460532	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646233	0.83[ASN][1000 genomes]
rs649200	0.86[ASN][1000 genomes]
rs6943309	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6951921	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6955261	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6961164	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6963882	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6966036	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6978134	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6979355	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6980307	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs726372	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7779010	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7786073	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7795152	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7796973	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7797340	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7801117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7809145	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7809303	0.83[ASN][1000 genomes]
rs7809934	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877687	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv492242	chr7:69330737-69520566	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1017390	chr7:69339404-69406232	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv538920	chr7:69339404-69406232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12333974	AUTS2	cis	cerebellum	SCAN
rs12333974	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69311400-69371600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69338400-69367200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:69351200-69375400	Weak transcription	Fetal Stomach	stomach
4	chr7:69355400-69368000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:69355400-69370600	Weak transcription	Fetal Brain Female	brain
6	chr7:69355400-69371200	Weak transcription	Brain Anterior Caudate	brain
7	chr7:69355400-69372000	Weak transcription	Adipose Nuclei	Adipose
8	chr7:69355400-69376600	Weak transcription	Ovary	ovary
9	chr7:69359000-69371400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:69359000-69372000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:69360600-69371400	Enhancers	Dnd41	blood
12	chr7:69361400-69367800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:69361400-69368000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:69361400-69371200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:69361400-69371200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:69361400-69373200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:69361600-69368000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:69361600-69371200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:69362000-69373000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:69363600-69367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:69365000-69371200	Weak transcription	Fetal Thymus	thymus
22	chr7:69365200-69370200	Weak transcription	GM12878-XiMat	blood
23	chr7:69366000-69369200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:69366000-69371200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:69366600-69369400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr7:69366600-69369400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:69366800-69371200	Weak transcription	Primary B cells from peripheral blood	blood

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