Variant report

Variant	rs10171331
Chromosome Location	chr2:54708408-54708409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10205013	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477221	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17039554	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17045917	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3087854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35001659	0.88[EUR][1000 genomes]
rs4233950	0.83[EUR][1000 genomes]
rs4561702	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4635562	0.81[EUR][1000 genomes]
rs4671218	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671933	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4671935	0.85[EUR][1000 genomes]
rs4671940	0.98[ASN][1000 genomes]
rs4671943	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58779052	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545409	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6718276	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754429	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72618659	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72618660	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72618661	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618662	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599380	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10171331	PSME4	cis	cerebellum	SCAN
rs10171331	VRK2	cis	cerebellum	SCAN
rs10171331	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54697200-54709600	Weak transcription	Placenta	Placenta
2	chr2:54699600-54709200	Weak transcription	Aorta	Aorta
3	chr2:54699800-54709600	Weak transcription	Osteobl	bone
4	chr2:54701400-54709800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
6	chr2:54702200-54712200	Enhancers	Fetal Heart	heart
7	chr2:54702400-54712000	Enhancers	Colon Smooth Muscle	Colon
8	chr2:54702800-54709000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:54703200-54708800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:54703600-54710400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:54703800-54709000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:54703800-54709000	Weak transcription	Fetal Brain Female	brain
13	chr2:54703800-54709200	Weak transcription	Right Ventricle	heart
14	chr2:54704400-54709000	Weak transcription	A549	lung
15	chr2:54704400-54710400	Enhancers	Right Atrium	heart
16	chr2:54705000-54709200	Enhancers	Liver	Liver
17	chr2:54705000-54710400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr2:54705200-54709600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:54705200-54709600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:54705200-54709800	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:54705200-54710000	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:54705200-54712400	Enhancers	Brain Hippocampus Middle	brain
23	chr2:54705400-54709600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:54705400-54710000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:54705600-54708600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:54705600-54708800	Weak transcription	Fetal Stomach	stomach
27	chr2:54705600-54709000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:54705600-54709600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:54705600-54710000	Weak transcription	Small Intestine	intestine
30	chr2:54705800-54709600	Weak transcription	HSMM	muscle
31	chr2:54705800-54709800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:54706400-54709200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:54706400-54709600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:54706800-54709600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:54706800-54709600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:54706800-54711600	Enhancers	HSMMtube	muscle
37	chr2:54707000-54710400	Enhancers	Fetal Muscle Leg	muscle
38	chr2:54707200-54708600	Enhancers	Fetal Lung	lung
39	chr2:54707200-54708600	Enhancers	Pancreas	Pancrea
40	chr2:54707200-54709000	Enhancers	Fetal Brain Male	brain
41	chr2:54707200-54710600	Enhancers	Brain Angular Gyrus	brain
42	chr2:54707200-54711200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:54707200-54711400	Enhancers	Ovary	ovary
44	chr2:54707200-54712000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:54707200-54712200	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:54707200-54712400	Enhancers	Brain Substantia Nigra	brain
47	chr2:54707400-54709200	Weak transcription	HepG2	liver
48	chr2:54707400-54709600	Weak transcription	Hela-S3	cervix
49	chr2:54707400-54709600	Weak transcription	HMEC	breast
50	chr2:54707400-54709600	Weak transcription	HUVEC	blood vessel

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