Variant report

Variant	rs11024061
Chromosome Location	chr11:16882049-16882050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11024054	1.00[ASW][hapmap];0.92[GIH][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap]
rs11024058	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024059	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]
rs11024069	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024071	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12222901	1.00[ASW][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.82[TSI][hapmap]
rs12223233	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12223369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12226273	0.86[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17698419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17772101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4756868	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4756870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4756871	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4757441	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[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55814202	0.83[AMR][1000 genomes]
rs56005045	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61496580	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72864090	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72864092	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72864100	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11024061	INSC	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16853400-16883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr11:16863800-16884800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr11:16863800-16892600	Weak transcription	Fetal Kidney	kidney
4	chr11:16867800-16885000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:16872000-16895800	Weak transcription	Aorta	Aorta
6	chr11:16872200-16882200	Weak transcription	Brain Angular Gyrus	brain
7	chr11:16872200-16884400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:16872600-16889600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:16872800-16883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:16876000-16883800	Weak transcription	Fetal Brain Female	brain
11	chr11:16876200-16888400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:16876400-16883600	Weak transcription	Spleen	Spleen
13	chr11:16876600-16884000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:16876600-16889800	Weak transcription	Adipose Nuclei	Adipose
15	chr11:16876600-16890800	Weak transcription	Colonic Mucosa	Colon
16	chr11:16876800-16898600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:16877800-16883800	Weak transcription	Brain Germinal Matrix	brain
18	chr11:16877800-16890000	Weak transcription	Lung	lung
19	chr11:16877800-16892200	Weak transcription	Fetal Stomach	stomach
20	chr11:16877800-16899600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:16878000-16889400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:16878200-16883800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:16878400-16883400	Weak transcription	Brain Substantia Nigra	brain
24	chr11:16878600-16882200	Weak transcription	Brain Anterior Caudate	brain
25	chr11:16878800-16890000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:16879000-16883600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:16879000-16884200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:16879000-16887600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:16879200-16883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:16879200-16884000	Weak transcription	Liver	Liver
31	chr11:16879400-16885000	Enhancers	K562	blood
32	chr11:16880400-16882400	Enhancers	Left Ventricle	heart
33	chr11:16880400-16883800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:16880400-16885200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:16880400-16885800	Enhancers	Fetal Muscle Leg	muscle
36	chr11:16880600-16882200	Enhancers	HMEC	breast
37	chr11:16880600-16882400	Enhancers	HepG2	liver
38	chr11:16881000-16882200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:16881000-16884600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:16881200-16882200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:16881400-16882400	Enhancers	Gastric	stomach
42	chr11:16881400-16882600	Flanking Active TSS	Fetal Heart	heart
43	chr11:16881400-16883000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr11:16881400-16883000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr11:16881600-16882200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:16881600-16882400	Enhancers	Brain Hippocampus Middle	brain
47	chr11:16881600-16882600	Enhancers	Fetal Intestine Large	intestine
48	chr11:16881800-16882200	Weak transcription	Placenta	Placenta
49	chr11:16881800-16882200	Weak transcription	Pancreas	Pancrea
50	chr11:16881800-16882400	Enhancers	Fetal Intestine Small	intestine

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