Variant report

Variant	rs11638793
Chromosome Location	chr15:62321476-62321477
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62320983..62322579-chr15:62345142..62347207,2	K562	blood:
2	chr15:62304589..62306825-chr15:62320734..62322432,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10851704	0.84[GIH][hapmap]
rs11071634	0.82[GIH][hapmap]
rs11071649	0.80[ASN][1000 genomes]
rs11630353	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632842	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11635621	0.89[EUR][1000 genomes]
rs11639482	0.81[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs12442448	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442589	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12442675	0.81[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs12591155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591156	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591593	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592402	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12594658	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12595300	0.89[EUR][1000 genomes]
rs12898209	0.89[GIH][hapmap];0.87[MEX][hapmap]
rs12901575	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12903649	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12917535	0.86[EUR][1000 genomes]
rs1370177	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs1436958	0.82[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs1436959	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1436965	0.85[CEU][hapmap]
rs1561197	0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs2162062	0.81[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs2414754	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs2414756	0.90[EUR][1000 genomes]
rs28837073	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2899678	0.87[EUR][1000 genomes]
rs35123892	0.81[ASN][1000 genomes]
rs3784445	0.82[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638519	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4775445	0.84[GIH][hapmap]
rs4775447	0.87[GIH][hapmap]
rs62007368	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7163326	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7163441	0.82[GIH][hapmap]
rs7164933	0.82[GIH][hapmap]
rs7168164	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs8023668	0.81[CEU][hapmap]
rs8025404	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8032433	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap]
rs893156	0.92[YRI][hapmap]
rs933807	0.92[YRI][hapmap]
rs9635310	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920758	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv516639	chr15:62175134-62340126	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv904293	chr15:62178695-62338797	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv904298	chr15:62218689-62338797	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv569648	chr15:62239697-62340126	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11638793	TEX9	cis	parietal	SCAN
rs11638793	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62185600-62333600	Weak transcription	Right Ventricle	heart
2	chr15:62221400-62327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:62244600-62350400	Weak transcription	Small Intestine	intestine
4	chr15:62259400-62327200	Weak transcription	HepG2	liver
5	chr15:62264000-62323800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:62264000-62324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:62265600-62338200	Weak transcription	Stomach Mucosa	stomach
8	chr15:62276400-62326800	Weak transcription	Thymus	Thymus
9	chr15:62276400-62345000	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:62276600-62327600	Weak transcription	NHLF	lung
11	chr15:62282200-62327800	Weak transcription	Colonic Mucosa	Colon
12	chr15:62287400-62322200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:62288600-62327600	Weak transcription	HMEC	breast
14	chr15:62288600-62336600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:62300000-62327600	Weak transcription	Hela-S3	cervix
16	chr15:62300000-62327800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:62300000-62334600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:62300200-62327600	Weak transcription	NH-A	brain
19	chr15:62300400-62351400	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:62300600-62322200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:62300600-62327600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:62300600-62327600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:62300600-62327600	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:62300600-62330600	Weak transcription	Aorta	Aorta
25	chr15:62300600-62330600	Weak transcription	Fetal Intestine Small	intestine
26	chr15:62300600-62337600	Weak transcription	Fetal Stomach	stomach
27	chr15:62300600-62342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:62300600-62345800	Weak transcription	Gastric	stomach
29	chr15:62300600-62351800	Weak transcription	Lung	lung
30	chr15:62300800-62324400	Weak transcription	Brain Germinal Matrix	brain
31	chr15:62300800-62327600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:62300800-62351600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:62301200-62322200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:62301400-62327600	Weak transcription	Osteobl	bone
35	chr15:62301600-62334400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:62301600-62336000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:62302200-62351600	Weak transcription	Fetal Thymus	thymus
38	chr15:62302200-62351600	Weak transcription	Ovary	ovary
39	chr15:62302400-62336200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:62302800-62333200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:62305800-62327200	Weak transcription	HUVEC	blood vessel
42	chr15:62306200-62321800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:62306200-62343600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:62307000-62327600	Weak transcription	Brain Substantia Nigra	brain
45	chr15:62312000-62328200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:62313200-62327400	Weak transcription	NHEK	skin
47	chr15:62313400-62323400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:62313400-62327600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:62313400-62327600	Weak transcription	A549	lung
50	chr15:62313400-62327800	Weak transcription	Rectal Smooth Muscle	rectum

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