Variant report

Variant	rs13226538
Chromosome Location	chr7:69420939-69420940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1014417	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10234205	0.87[AMR][1000 genomes]
rs10235487	0.85[ASN][1000 genomes]
rs10235781	0.81[ASN][1000 genomes]
rs10235860	0.80[AMR][1000 genomes]
rs10245786	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10257549	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259748	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10268235	0.85[ASN][1000 genomes]
rs10268924	0.82[ASN][1000 genomes]
rs10270616	0.87[AMR][1000 genomes]
rs10273270	0.86[AMR][1000 genomes]
rs1035010	0.85[ASN][1000 genomes]
rs1035013	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10452738	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11508453	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11761141	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11763186	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11767997	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11974201	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11978431	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333974	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12698813	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698816	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12698822	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12698825	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12698830	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12698842	0.83[AMR][1000 genomes]
rs12698849	0.81[AMR][1000 genomes]
rs12698855	0.85[ASN][1000 genomes]
rs12698871	0.82[ASN][1000 genomes]
rs13228123	0.85[ASN][1000 genomes]
rs13237811	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558413	0.86[AMR][1000 genomes]
rs17140933	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17140980	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140982	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210591	0.82[ASN][1000 genomes]
rs210593	0.82[ASN][1000 genomes]
rs210596	0.82[ASN][1000 genomes]
rs210601	0.82[ASN][1000 genomes]
rs210604	0.82[ASN][1000 genomes]
rs210606	0.81[ASN][1000 genomes]
rs2159678	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2865805	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2866075	0.83[AMR][1000 genomes]
rs28770244	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221396	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34617709	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35222730	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35696945	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717520	0.81[ASN][1000 genomes]
rs55990156	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60359704	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6415223	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6460532	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6460536	0.86[ASN][1000 genomes]
rs6460537	0.82[ASN][1000 genomes]
rs6651055	0.82[ASN][1000 genomes]
rs6943309	0.82[AMR][1000 genomes]
rs6944725	0.87[AMR][1000 genomes]
rs6949651	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6950485	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6950647	0.82[ASN][1000 genomes]
rs6951921	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953170	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6955261	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6958981	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6961164	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6961345	0.82[ASN][1000 genomes]
rs6962999	0.86[ASN][1000 genomes]
rs6963882	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963904	0.85[AMR][1000 genomes]
rs6966036	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6974687	0.85[AMR][1000 genomes]
rs6975279	0.82[ASN][1000 genomes]
rs6978134	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6979355	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6980307	0.81[AMR][1000 genomes]
rs726372	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73442405	0.87[AMR][1000 genomes]
rs7779010	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7784584	0.81[ASN][1000 genomes]
rs7786073	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7790729	0.82[ASN][1000 genomes]
rs7791101	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7794623	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7795152	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796080	0.82[ASN][1000 genomes]
rs7796973	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7797340	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7805470	0.81[ASN][1000 genomes]
rs7809145	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7809303	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7809934	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870920	0.81[ASN][1000 genomes]
rs873835	0.81[ASN][1000 genomes]
rs877687	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[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	nsv916265	chr7:69367265-69433076	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1031593	chr7:69367316-69445052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv538921	chr7:69367316-69445052	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13226538	VKORC1L1	cis	parietal	SCAN
rs13226538	AUTS2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69404600-69427800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:69411000-69426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:69414800-69423400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:69415000-69427200	Weak transcription	Fetal Kidney	kidney
5	chr7:69415800-69422800	Weak transcription	Left Ventricle	heart
6	chr7:69416400-69424000	Enhancers	Fetal Thymus	thymus
7	chr7:69417200-69421800	Enhancers	Thymus	Thymus
8	chr7:69418000-69427000	Weak transcription	Adipose Nuclei	Adipose
9	chr7:69418200-69424800	Weak transcription	Fetal Brain Female	brain
10	chr7:69418400-69422800	Weak transcription	Right Atrium	heart
11	chr7:69418400-69424800	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:69418600-69421400	Enhancers	Primary T cells from cord blood	blood
13	chr7:69418600-69426800	Weak transcription	Brain Angular Gyrus	brain
14	chr7:69418600-69427000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:69418800-69422800	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:69418800-69426800	Weak transcription	Brain Anterior Caudate	brain
17	chr7:69419200-69421000	Enhancers	Dnd41	blood
18	chr7:69419600-69422600	Weak transcription	Psoas Muscle	Psoas
19	chr7:69419600-69422800	Weak transcription	Right Ventricle	heart
20	chr7:69419600-69422800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:69419600-69426800	Weak transcription	Fetal Stomach	stomach
22	chr7:69419800-69423400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:69419800-69423400	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:69419800-69423800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:69420000-69423800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:69420000-69424400	Weak transcription	Fetal Brain Male	brain
27	chr7:69420400-69422600	Weak transcription	Fetal Heart	heart
28	chr7:69420400-69423800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:69420400-69426800	Weak transcription	GM12878-XiMat	blood
30	chr7:69420800-69423400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr7:69420800-69423400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:69420800-69423600	Weak transcription	Primary B cells from cord blood	blood

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