Variant report

Variant	rs3748223
Chromosome Location	chr10:25231171-25231172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25230623..25233059-chr10:25234068..25237014,2	K562	blood:
2	chr10:25228270..25233826-chr10:25234068..25237911,6	K562	blood:
3	chr10:25229734..25232963-chr10:25239318..25242325,3	K562	blood:
4	chr10:25219739..25221731-chr10:25228623..25231454,2	K562	blood:

Variant related genes	Relation type
ENSG00000099256	Chromatin interaction
ENSG00000273107	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10741071	0.89[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10741072	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10764513	0.84[ASN][1000 genomes]
rs10828727	1.00[YRI][hapmap]
rs10828728	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10828730	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10828731	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11014314	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11014318	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014319	0.83[ASW][hapmap]
rs11014320	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs185669	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.89[ASN][1000 genomes]
rs2035888	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2478091	0.92[ASN][1000 genomes]
rs274295	0.80[ASN][1000 genomes]
rs274296	0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs274297	0.81[ASN][1000 genomes]
rs274299	0.92[ASN][1000 genomes]
rs274301	0.83[JPT][hapmap]
rs274305	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs274307	0.83[ASN][1000 genomes]
rs274310	0.83[ASN][1000 genomes]
rs274311	0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs274313	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs274316	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3000491	0.83[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	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3748223	OTUD1	cis	parietal	SCAN
rs3748223	ARMC3	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25191600-25240600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:25210400-25236600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:25210600-25233400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:25210600-25233400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:25211400-25239800	Weak transcription	Fetal Kidney	kidney
6	chr10:25215800-25240000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:25218600-25233400	Weak transcription	NHLF	lung
8	chr10:25218800-25236600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:25219000-25236600	Weak transcription	Ovary	ovary
10	chr10:25219200-25233600	Weak transcription	NHDF-Ad	bronchial
11	chr10:25219200-25240000	Weak transcription	Dnd41	blood
12	chr10:25219800-25233200	Weak transcription	A549	lung
13	chr10:25221400-25233800	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:25223600-25233400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:25224200-25236400	Weak transcription	Brain Germinal Matrix	brain
16	chr10:25224400-25233400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:25224600-25236000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr10:25225400-25233000	Weak transcription	Fetal Intestine Large	intestine
19	chr10:25225400-25240000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:25225400-25240000	Weak transcription	Fetal Brain Female	brain
21	chr10:25225800-25232800	Weak transcription	Fetal Intestine Small	intestine
22	chr10:25225800-25233600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:25226000-25233200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:25226200-25239800	Weak transcription	Fetal Lung	lung
25	chr10:25226400-25232200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:25226400-25239200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:25227600-25233600	Weak transcription	Brain Anterior Caudate	brain
28	chr10:25227600-25236600	Weak transcription	Pancreas	Pancrea
29	chr10:25227800-25233800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr10:25227800-25233800	Weak transcription	Brain Substantia Nigra	brain
31	chr10:25227800-25235400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:25227800-25235800	Weak transcription	Brain Angular Gyrus	brain
33	chr10:25228000-25232800	Weak transcription	K562	blood
34	chr10:25228000-25233800	Weak transcription	Brain Hippocampus Middle	brain
35	chr10:25228000-25235600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:25228200-25232200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:25228200-25239800	Weak transcription	Fetal Stomach	stomach
38	chr10:25229800-25236600	Weak transcription	Fetal Muscle Leg	muscle
39	chr10:25230000-25233600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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