Variant report

Variant	rs1493699
Chromosome Location	chr15:77664901-77664902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77664650..77667027-chr15:77668705..77670946,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10162778	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11853696	0.88[ASN][1000 genomes]
rs11856084	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11857330	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12324016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324211	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324366	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12324795	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12912084	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13380202	0.92[ASN][1000 genomes]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs1446313	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs16968730	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16968799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384809	0.92[ASN][1000 genomes]
rs17385059	0.92[ASN][1000 genomes]
rs17385296	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17385352	0.92[ASN][1000 genomes]
rs17470529	0.90[ASN][1000 genomes]
rs17470952	0.86[ASN][1000 genomes]
rs17471252	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471431	0.83[ASN][1000 genomes]
rs17471480	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs17471697	0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs17471753	0.81[ASN][1000 genomes]
rs2012740	0.83[ASN][1000 genomes]
rs2012756	0.83[ASN][1000 genomes]
rs2172587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2307141	0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs28437977	0.90[ASN][1000 genomes]
rs2864840	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34572155	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs35651077	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784787	0.90[ASN][1000 genomes]
rs3784788	0.93[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4592615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4886863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886864	0.90[ASN][1000 genomes]
rs4886865	0.90[ASN][1000 genomes]
rs59362734	0.82[ASN][1000 genomes]
rs59386622	0.83[ASN][1000 genomes]
rs62007297	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62010566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163620	0.83[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs74026910	0.84[ASN][1000 genomes]
rs74026912	0.86[ASN][1000 genomes]
rs74026913	0.87[ASN][1000 genomes]
rs74026918	0.81[ASN][1000 genomes]
rs74026926	0.80[ASN][1000 genomes]
rs8029163	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035526	0.90[ASN][1000 genomes]
rs883627	0.92[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs907398	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9806326	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1836778	chr15:77608747-77694607	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1795063	chr15:77628696-77697976	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv1801694	chr15:77658980-77673459	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1803922	chr15:77659787-77673170	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1794286	chr15:77660093-77673459	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1799610	chr15:77660093-77673776	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv1801387	chr15:77660093-77673776	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	esv1801597	chr15:77660093-77673776	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv1802961	chr15:77660093-77673776	Genic enhancers Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv1803817	chr15:77660093-77673776	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv1796028	chr15:77660345-77673420	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	esv2761954	chr15:77660345-77676969	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv17840	chr15:77660974-77673898	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	esv1793848	chr15:77662140-77676568	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	esv1795034	chr15:77664889-77673459	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	esv1804031	chr15:77664889-77673459	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv1794292	chr15:77664889-77673776	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv1800284	chr15:77664889-77673776	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv1801957	chr15:77664889-77673776	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv1801996	chr15:77664889-77673776	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv1803767	chr15:77664889-77673776	Genic enhancers Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	esv1800929	chr15:77664889-77697976	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
32	nsv570132	chr15:77664901-77672777	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv570133	chr15:77664901-77673359	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
34	esv1803365	chr15:77664901-77673459	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
35	esv1803655	chr15:77664901-77673459	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv570134	chr15:77664901-77673459	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
37	esv1801192	chr15:77664901-77673776	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv570135	chr15:77664901-77673776	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
39	esv1792043	chr15:77664901-77708316	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1493699	CYP1A2	cis	cerebellum	SCAN
rs1493699	HMG20A	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77637200-77666800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:77639800-77687000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:77645800-77665800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:77645800-77665800	Weak transcription	Pancreas	Pancrea
5	chr15:77645800-77674000	Weak transcription	Ovary	ovary
6	chr15:77645800-77677000	Weak transcription	Right Ventricle	heart
7	chr15:77646800-77666000	Weak transcription	Stomach Mucosa	stomach
8	chr15:77647000-77687200	Weak transcription	A549	lung
9	chr15:77648600-77685800	Weak transcription	Gastric	stomach
10	chr15:77651600-77674000	Weak transcription	Psoas Muscle	Psoas
11	chr15:77656000-77666000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:77656000-77674000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:77656200-77676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:77656400-77665200	Weak transcription	Left Ventricle	heart
15	chr15:77656400-77683200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:77656600-77665600	Weak transcription	Fetal Stomach	stomach
17	chr15:77660400-77671000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:77662000-77667400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:77662200-77677000	Weak transcription	NHDF-Ad	bronchial
20	chr15:77663000-77680200	Weak transcription	Osteobl	bone
21	chr15:77664000-77665000	Enhancers	Fetal Heart	heart
22	chr15:77664000-77665200	Enhancers	Brain Germinal Matrix	brain
23	chr15:77664200-77665000	Enhancers	Brain Anterior Caudate	brain
24	chr15:77664200-77665200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:77664400-77665000	Enhancers	Brain Cingulate Gyrus	brain
26	chr15:77664400-77665000	Enhancers	Brain Hippocampus Middle	brain
27	chr15:77664400-77665000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr15:77664600-77678200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:77664800-77665000	Enhancers	Duodenum Smooth Muscle	Duodenum

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