Variant report

Variant	rs2159678
Chromosome Location	chr7:69488331-69488332
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10234205	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10235487	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10235860	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10251306	0.87[ASN][1000 genomes]
rs10256186	0.88[ASN][1000 genomes]
rs10257549	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10268235	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10270616	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10273270	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10279392	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1035010	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1035013	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10452738	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10499812	0.88[ASN][1000 genomes]
rs11761141	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11767997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11978431	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12698816	0.80[AMR][1000 genomes]
rs12698822	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12698825	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12698830	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12698835	0.80[EUR][1000 genomes]
rs12698842	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698849	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12698866	0.88[ASN][1000 genomes]
rs12698877	0.82[ASN][1000 genomes]
rs13226538	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13237811	0.81[AMR][1000 genomes]
rs1558413	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866075	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28770244	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34617709	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35222730	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35696945	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6415223	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6460536	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6944725	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6949651	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6950485	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6951921	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6953170	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6957126	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6958981	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6961164	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6962999	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6963904	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6966036	0.80[AMR][1000 genomes]
rs6969375	0.80[ASN][1000 genomes]
rs6974687	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6979355	0.80[AMR][1000 genomes]
rs73442405	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7781035	0.83[ASN][1000 genomes]
rs7788024	0.83[ASN][1000 genomes]
rs7790934	0.83[ASN][1000 genomes]
rs7791101	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7794623	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7795152	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7797340	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7808540	0.83[ASN][1000 genomes]
rs7809303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7809934	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9638268	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv1018289	chr7:69383450-69650885	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv538922	chr7:69383450-69650885	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1034281	chr7:69403828-69548378	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv538923	chr7:69403828-69548378	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1034182	chr7:69406172-69529294	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv538924	chr7:69406172-69529294	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2758119	chr7:69412504-69594161	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2759536	chr7:69412504-69594161	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv607429	chr7:69430748-69553093	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1028705	chr7:69453983-69524628	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1020488	chr7:69465268-69671126	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2159678	AUTS2	cis	cerebellum	SCAN
rs2159678	VKORC1L1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69477200-69490400	Weak transcription	Left Ventricle	heart
2	chr7:69477200-69507600	Weak transcription	Right Atrium	heart
3	chr7:69478600-69491000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:69479800-69494000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:69481600-69488400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:69482600-69490400	Weak transcription	Fetal Thymus	thymus
7	chr7:69482600-69491000	Weak transcription	Psoas Muscle	Psoas
8	chr7:69482800-69489600	Weak transcription	Fetal Stomach	stomach
9	chr7:69482800-69490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:69483400-69488800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:69483400-69495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:69486400-69488800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:69486400-69494000	Enhancers	Fetal Heart	heart
14	chr7:69486800-69488600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:69487000-69490800	Weak transcription	Brain Germinal Matrix	brain
16	chr7:69487000-69491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:69487000-69491000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:69487000-69491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:69487000-69495800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:69487000-69496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:69487000-69497600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr7:69487200-69489200	Weak transcription	Fetal Brain Male	brain
23	chr7:69487200-69491200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:69487200-69491200	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:69487600-69488800	Weak transcription	Fetal Brain Female	brain
26	chr7:69488200-69488600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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