Variant report

Variant	rs11635308
Chromosome Location	chr15:49718728-49718729
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1023683	0.81[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519221	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519226	0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519227	0.82[ASW][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1055254	0.81[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs11630318	1.00[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632303	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632575	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633282	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635005	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635354	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635814	1.00[ASN][1000 genomes]
rs11638314	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638515	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs11638606	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639423	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592277	0.82[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12913966	1.00[ASN][1000 genomes]
rs17396119	0.93[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396536	0.93[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396612	0.88[MEX][hapmap];0.80[TSI][hapmap]
rs17396747	0.93[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397211	0.93[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400427	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400706	0.91[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17400916	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476940	0.81[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs17477722	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17477923	0.83[ASW][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs17478618	0.91[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479003	0.93[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479205	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17479289	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2078024	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs28393768	1.00[ASN][1000 genomes]
rs28408092	1.00[ASN][1000 genomes]
rs28409376	1.00[ASN][1000 genomes]
rs28430272	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28484276	1.00[ASN][1000 genomes]
rs28669217	1.00[ASN][1000 genomes]
rs35692325	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338740	0.81[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs57252806	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57749497	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	1.00[ASN][1000 genomes]
rs59112977	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59356430	0.81[EUR][1000 genomes]
rs60594237	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61259878	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165168	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167474	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168316	0.82[ASW][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7177624	1.00[ASN][1000 genomes]
rs73390384	1.00[ASN][1000 genomes]
rs73390392	1.00[ASN][1000 genomes]
rs73392236	1.00[ASN][1000 genomes]
rs73392249	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392256	1.00[ASN][1000 genomes]
rs73392277	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392288	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394324	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394331	0.90[EUR][1000 genomes]
rs73394333	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394339	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394355	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394359	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396206	0.81[EUR][1000 genomes]
rs73396235	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396238	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398223	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398243	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398264	0.83[AFR][1000 genomes]
rs73398272	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398276	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73398284	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400205	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8027094	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030457	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033311	0.81[EUR][1000 genomes]
rs8040716	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11635308	SECISBP2L	cis	cerebellum	SCAN
rs11635308	TNFAIP8L3	cis	parietal	SCAN
rs11635308	TRPM7	cis	cerebellum	SCAN
rs11635308	FGF7	cis	Muscle Skeletal	GTEx
rs11635308	MFAP1	cis	cerebellum	SCAN
rs11635308	SECISBP2L	cis	parietal	SCAN
rs11635308	LCMT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49714000-49720400	Active TSS	Ovary	ovary
2	chr15:49714000-49720800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:49714000-49721000	Active TSS	Colon Smooth Muscle	Colon
4	chr15:49714000-49722600	Active TSS	Stomach Smooth Muscle	stomach
5	chr15:49714200-49719400	Active TSS	Fetal Kidney	kidney
6	chr15:49714200-49721000	Active TSS	Rectal Smooth Muscle	rectum
7	chr15:49714200-49721000	Active TSS	Right Atrium	heart
8	chr15:49714200-49721400	Active TSS	Adipose Nuclei	Adipose
9	chr15:49714800-49720600	Active TSS	NHDF-Ad	bronchial
10	chr15:49715200-49719200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr15:49715200-49719400	Active TSS	Fetal Muscle Leg	muscle
12	chr15:49715200-49719400	Active TSS	Right Ventricle	heart
13	chr15:49715200-49719600	Active TSS	Osteobl	bone
14	chr15:49715200-49720000	Active TSS	Fetal Stomach	stomach
15	chr15:49715400-49721600	Active TSS	NHLF	lung
16	chr15:49716200-49732200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:49716800-49720600	Weak transcription	Psoas Muscle	Psoas
19	chr15:49716800-49720600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:49716800-49720800	Weak transcription	Hela-S3	cervix
21	chr15:49716800-49722000	Weak transcription	Colonic Mucosa	Colon
22	chr15:49717000-49720400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:49717000-49721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:49717400-49720200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:49717600-49721200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:49718000-49719000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:49718000-49719400	Weak transcription	Fetal Lung	lung
28	chr15:49718000-49727800	Weak transcription	HSMMtube	muscle
29	chr15:49718000-49731200	Weak transcription	Left Ventricle	heart
30	chr15:49718600-49719000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:49718600-49719400	Enhancers	Fetal Heart	heart
32	chr15:49718600-49719600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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