Variant report

Variant	rs11635005
Chromosome Location	chr15:49601425-49601426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1023683	0.81[CEU][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10519221	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519226	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10519227	0.82[ASW][hapmap]
rs1055254	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11630318	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632211	1.00[ASN][1000 genomes]
rs11632303	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632575	0.93[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633282	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635308	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];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635455	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635814	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638314	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638515	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11638606	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639423	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12592277	0.81[EUR][1000 genomes]
rs12913966	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394420	0.93[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394970	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396119	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396536	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396612	1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs17396747	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397211	0.93[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400427	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17400706	0.90[ASW][hapmap];0.93[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17400916	1.00[ASN][1000 genomes]
rs17473148	0.93[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473568	0.93[CEU][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17475228	0.83[EUR][1000 genomes]
rs17476361	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476940	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs17477722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478618	0.90[ASW][hapmap];0.93[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479003	0.93[CEU][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078024	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs28393768	1.00[ASN][1000 genomes]
rs28408092	1.00[ASN][1000 genomes]
rs28409376	1.00[ASN][1000 genomes]
rs28430272	1.00[ASN][1000 genomes]
rs28484276	1.00[ASN][1000 genomes]
rs28669217	1.00[ASN][1000 genomes]
rs3088333	0.93[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34606419	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35692325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57252806	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57749497	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785991	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59112977	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59356430	0.82[EUR][1000 genomes]
rs60594237	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61259878	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61442055	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165168	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167474	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168316	0.82[ASW][hapmap]
rs7168633	0.83[EUR][1000 genomes]
rs7177624	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390343	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390360	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390362	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390384	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73390392	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392236	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392249	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392256	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392277	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392288	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394324	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394331	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73394333	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394339	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394355	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394357	0.86[EUR][1000 genomes]
rs73394359	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396206	0.82[EUR][1000 genomes]
rs73396235	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396238	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398223	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398243	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398276	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73398284	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73408143	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025550	0.94[MEX][hapmap];0.83[TSI][hapmap]
rs8027094	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029506	0.85[EUR][1000 genomes]
rs8030457	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033311	0.82[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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11635005	TRPM7	cis	cerebellum	SCAN
rs11635005	SECISBP2L	cis	parietal	SCAN
rs11635005	SECISBP2L	cis	cerebellum	SCAN
rs11635005	MFAP1	cis	cerebellum	SCAN
rs11635005	TNFAIP8L3	cis	parietal	SCAN
rs11635005	FGF7	cis	Muscle Skeletal	GTEx
rs11635005	TMEM62	cis	cerebellum	SCAN
rs11635005	LCMT2	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
4	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
5	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
8	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
11	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
14	chr15:49577000-49605800	Weak transcription	A549	lung
15	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
17	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
18	chr15:49578200-49604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:49578200-49611000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:49578400-49605400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:49578400-49611200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:49579400-49612000	Weak transcription	HUVEC	blood vessel
23	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
24	chr15:49580800-49605600	Weak transcription	NHEK	skin
25	chr15:49581200-49607400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:49581400-49607600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:49582200-49611400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
29	chr15:49583000-49606800	Weak transcription	Fetal Stomach	stomach
30	chr15:49583200-49611400	Weak transcription	Small Intestine	intestine
31	chr15:49584000-49605800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:49584000-49607400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:49584000-49607400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:49585600-49607200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:49585600-49612800	Weak transcription	Fetal Thymus	thymus
36	chr15:49586000-49617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:49586200-49611200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:49588800-49607400	Weak transcription	Brain Substantia Nigra	brain
39	chr15:49588800-49611200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:49588800-49611600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:49589200-49607400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:49594000-49619400	Weak transcription	Stomach Mucosa	stomach
43	chr15:49594200-49605600	Weak transcription	HMEC	breast
44	chr15:49594400-49605400	Weak transcription	Osteobl	bone
45	chr15:49594600-49607600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:49595800-49611200	Weak transcription	Aorta	Aorta
47	chr15:49596000-49604200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:49596200-49611400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:49596800-49605200	Weak transcription	NHLF	lung
50	chr15:49596800-49605400	Weak transcription	Stomach Smooth Muscle	stomach

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