Variant report

Variant	rs4936578
Chromosome Location	chr11:120999258-120999259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10892676	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11218148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11218158	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11218160	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11826847	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12275038	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12279811	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12280641	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12285467	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12285468	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12288505	0.83[EUR][1000 genomes]
rs17245810	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1939934	0.85[EUR][1000 genomes]
rs1941299	1.00[CHB][hapmap]
rs1943656	0.83[EUR][1000 genomes]
rs34002948	0.93[EUR][1000 genomes]
rs34217740	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4427574	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4499012	0.88[EUR][1000 genomes]
rs4539330	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4623911	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4641485	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs489985	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4935760	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4935762	0.81[EUR][1000 genomes]
rs4936576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4936579	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4936582	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936583	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936584	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936585	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936586	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936587	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4936590	0.90[EUR][1000 genomes]
rs4936591	0.88[EUR][1000 genomes]
rs513182	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs524392	0.85[EUR][1000 genomes]
rs528958	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs541623	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs580683	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs581786	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs606674	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs607014	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs607999	0.93[EUR][1000 genomes]
rs615697	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs616184	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs620164	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs620778	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs624428	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs665743	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs667125	1.00[YRI][hapmap]
rs688106	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7105356	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7108587	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7108594	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7108741	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7108971	1.00[CHB][hapmap]
rs7110565	0.84[EUR][1000 genomes]
rs7114879	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7114915	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7120647	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7122110	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7125224	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128792	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7130952	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs877538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9651697	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9736671	0.90[EUR][1000 genomes]
rs9943635	0.84[EUR][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	nsv524	chr11:120963503-121008167	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4936578	VPS11	cis	cerebellum	SCAN
rs4936578	TAGLN	cis	cerebellum	SCAN
rs4936578	HINFP	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120975800-121005600	Weak transcription	Right Ventricle	heart
2	chr11:120993200-121008000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:120993800-121000600	Weak transcription	Fetal Stomach	stomach
4	chr11:120994000-121016200	Weak transcription	Brain Substantia Nigra	brain
5	chr11:120994200-120999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:120994400-121042400	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:120994600-121000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:120996400-121005200	Weak transcription	HSMMtube	muscle
9	chr11:120996800-121005400	Weak transcription	Left Ventricle	heart
10	chr11:120996800-121016400	Weak transcription	Ovary	ovary
11	chr11:120996800-121037800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:120997200-121005000	Weak transcription	Right Atrium	heart
13	chr11:120998000-121002400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:120998200-121001600	Weak transcription	Fetal Intestine Small	intestine
15	chr11:120998400-120999600	Strong transcription	Brain Anterior Caudate	brain
16	chr11:120998400-121000000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr11:120998400-121001000	Strong transcription	Fetal Brain Female	brain
18	chr11:120998400-121007800	Weak transcription	Fetal Brain Male	brain
19	chr11:120998600-120999400	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:120998600-120999600	Strong transcription	Brain Germinal Matrix	brain
21	chr11:120998800-121007800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:120998800-121009400	Weak transcription	Spleen	Spleen
23	chr11:120999000-121000600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:120999000-121007800	Weak transcription	Gastric	stomach
25	chr11:120999000-121011200	Weak transcription	Aorta	Aorta
26	chr11:120999200-121016200	Weak transcription	Brain Cingulate Gyrus	brain

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