Variant report

Variant	rs833364
Chromosome Location	chr10:93837134-93837135
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10509640	0.84[JPT][hapmap]
rs10786026	0.88[JPT][hapmap]
rs10882019	0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1104012	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs11186825	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186828	0.90[ASN][1000 genomes]
rs11817194	0.84[JPT][hapmap]
rs11818152	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12254369	0.84[JPT][hapmap]
rs12256118	0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263532	0.93[JPT][hapmap]
rs1229580	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17107472	1.00[JPT][hapmap]
rs1711850	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935864	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2048901	0.84[JPT][hapmap]
rs2252200	0.84[JPT][hapmap]
rs2676824	0.84[JPT][hapmap]
rs2792019	0.84[JPT][hapmap]
rs2797645	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4486531	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4509678	0.84[JPT][hapmap]
rs4642987	0.84[JPT][hapmap]
rs55737168	0.80[ASN][1000 genomes]
rs55901992	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6583801	0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070076	0.84[JPT][hapmap]
rs7077333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7093730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73314327	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7909870	0.84[JPT][hapmap]
rs7911552	0.84[JPT][hapmap]
rs7912721	0.88[JPT][hapmap]
rs7916626	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917088	0.81[ASW][hapmap];0.82[MKK][hapmap]
rs833365	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs833368	0.84[JPT][hapmap]
rs833380	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833386	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932820	0.81[ASW][hapmap]
rs9787645	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs833364	BTAF1	cis	cerebellum	SCAN
rs833364	CPEB3	cis	cerebellum	SCAN
rs833364	BTAF1	cis	parietal	SCAN
rs833364	SLC16A12	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93787400-93840000	Weak transcription	Small Intestine	intestine
2	chr10:93791800-93838400	Weak transcription	Brain Substantia Nigra	brain
3	chr10:93792800-93837800	Weak transcription	Brain Angular Gyrus	brain
4	chr10:93794400-93837200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:93796200-93840800	Weak transcription	Psoas Muscle	Psoas
6	chr10:93808000-93842600	Weak transcription	Fetal Lung	lung
7	chr10:93808200-93842800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:93808400-93844400	Weak transcription	Primary T cells from cord blood	blood
9	chr10:93812400-93837800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr10:93812800-93837200	Weak transcription	Ovary	ovary
11	chr10:93812800-93837800	Weak transcription	Brain Hippocampus Middle	brain
12	chr10:93812800-93837800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:93812800-93838200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:93812800-93838800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr10:93812800-93839800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:93812800-93840600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr10:93815400-93838200	Weak transcription	Primary B cells from cord blood	blood
18	chr10:93815400-93847200	Weak transcription	Hela-S3	cervix
19	chr10:93816800-93838600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:93817000-93842600	Weak transcription	Gastric	stomach
21	chr10:93817200-93838200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:93817600-93837600	Weak transcription	Left Ventricle	heart
23	chr10:93817600-93838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:93817600-93838600	Weak transcription	Fetal Stomach	stomach
25	chr10:93817600-93840000	Weak transcription	Spleen	Spleen
26	chr10:93817600-93840200	Weak transcription	Esophagus	oesophagus
27	chr10:93817600-93840400	Weak transcription	Fetal Intestine Small	intestine
28	chr10:93817600-93840800	Weak transcription	Lung	lung
29	chr10:93823200-93842400	Weak transcription	Colon Smooth Muscle	Colon
30	chr10:93823800-93840000	Weak transcription	Fetal Intestine Large	intestine
31	chr10:93824400-93842600	Weak transcription	Right Ventricle	heart
32	chr10:93824800-93842600	Weak transcription	HSMMtube	muscle
33	chr10:93828400-93840000	Weak transcription	Fetal Heart	heart
34	chr10:93828800-93838400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:93828800-93843000	Weak transcription	Osteobl	bone
36	chr10:93830400-93840800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:93831800-93842600	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:93832200-93842200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr10:93832400-93840600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr10:93833400-93842800	Weak transcription	Thymus	Thymus
41	chr10:93834400-93840600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:93834400-93841400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:93834400-93843400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:93835000-93837200	Weak transcription	Liver	Liver
45	chr10:93835000-93838400	Weak transcription	Brain Anterior Caudate	brain
46	chr10:93835000-93838400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:93835200-93837800	Weak transcription	Adipose Nuclei	Adipose
48	chr10:93835200-93839200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr10:93835200-93840000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr10:93835200-93840200	Weak transcription	Brain Cingulate Gyrus	brain

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