Variant report

Variant	rs12576839
Chromosome Location	chr11:47082464-47082465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12574558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578030	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17197500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17197710	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17790246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17790306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17790336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17790342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17790390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17790420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3751097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4572092	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647713	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4647736	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs55968738	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57012996	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57964319	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59689332	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60041842	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs60088916	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60174717	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60201196	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60335739	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61142746	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896124	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896125	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896126	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896131	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61896132	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897776	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897777	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897782	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61897784	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61897786	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61897788	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61897791	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61897851	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897852	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897853	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61897854	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61897855	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61897856	0.93[ASN][1000 genomes]
rs61897858	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61899284	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61899285	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61899293	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61899294	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[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	nsv1043108	chr11:47041565-47117248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv508627	chr11:47052659-47084007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12576839	CHST1	cis	parietal	SCAN
rs12576839	ATG13	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47061400-47082800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:47068400-47092400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:47071600-47089000	Weak transcription	Gastric	stomach
4	chr11:47072600-47093000	Weak transcription	Ovary	ovary
5	chr11:47072800-47093000	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:47073200-47082600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:47073200-47092400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:47073600-47088600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:47073800-47083800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:47073800-47092200	Weak transcription	Placenta	Placenta
11	chr11:47073800-47100200	Weak transcription	Thymus	Thymus
12	chr11:47074600-47082800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:47075200-47087400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:47075200-47093400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:47075400-47082800	Weak transcription	Esophagus	oesophagus
16	chr11:47075800-47093400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:47077600-47085800	Weak transcription	HepG2	liver
18	chr11:47077600-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:47077800-47088200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:47078000-47097000	Weak transcription	Aorta	Aorta
21	chr11:47078200-47093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:47078400-47092400	Weak transcription	Small Intestine	intestine
23	chr11:47078600-47092600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:47079400-47093000	Weak transcription	Fetal Brain Male	brain
25	chr11:47079800-47086600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:47080000-47092400	Weak transcription	Fetal Intestine Small	intestine
27	chr11:47080000-47092400	Weak transcription	Fetal Stomach	stomach
28	chr11:47080400-47090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:47080600-47083200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:47080600-47093200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:47080800-47084200	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:47080800-47103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:47081000-47082600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:47081000-47092400	Weak transcription	Fetal Intestine Large	intestine
35	chr11:47081200-47089000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:47081400-47085200	Weak transcription	Fetal Lung	lung
37	chr11:47081600-47083600	Enhancers	K562	blood
38	chr11:47082000-47082800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:47082000-47082800	Enhancers	Osteobl	bone
40	chr11:47082000-47083200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr11:47082000-47083400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr11:47082000-47083400	Enhancers	Primary hematopoietic stem cells	blood
43	chr11:47082000-47083600	Enhancers	HSMM	muscle
44	chr11:47082000-47083600	Enhancers	HSMMtube	muscle
45	chr11:47082000-47084400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:47082000-47084600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:47082000-47084600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr11:47082000-47084600	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr11:47082200-47082600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:47082200-47082800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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