Variant report

Variant	rs10021296
Chromosome Location	chr4:99483238-99483239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10002696	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10006366	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10018825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10025051	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs11730384	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs13108940	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs13134231	0.94[JPT][hapmap]
rs13141997	0.96[CEU][hapmap]
rs13149070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534554	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1534555	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1573478	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1919211	0.89[JPT][hapmap]
rs2037832	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap]
rs2866016	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2866017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699343	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699345	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs4699348	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs4699349	0.92[CEU][hapmap]
rs4699639	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699640	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4699644	0.96[CEU][hapmap]
rs4699650	0.89[JPT][hapmap]
rs6532742	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs6532748	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs6532751	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs6831643	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs6837359	0.92[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7672134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678323	0.84[CHB][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10021296	TSPAN5	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99477400-99486800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99477400-99487600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:99477400-99487600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:99479000-99486800	Weak transcription	Fetal Lung	lung
6	chr4:99479000-99490200	Weak transcription	HSMMtube	muscle
7	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
8	chr4:99479200-99484400	Weak transcription	HUVEC	blood vessel
9	chr4:99479200-99486800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:99479200-99486800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:99479200-99487000	Weak transcription	NH-A	brain
12	chr4:99479200-99487200	Weak transcription	NHLF	lung
13	chr4:99479800-99485800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:99479800-99486800	Weak transcription	Spleen	Spleen
15	chr4:99479800-99487000	Weak transcription	NHDF-Ad	bronchial
16	chr4:99480000-99486800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:99480200-99486000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:99480200-99486000	Weak transcription	Ovary	ovary
19	chr4:99480200-99486000	Weak transcription	Thymus	Thymus
20	chr4:99480400-99486800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:99480400-99487200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:99480600-99486200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:99481200-99485600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:99481200-99486800	Weak transcription	Brain Germinal Matrix	brain
25	chr4:99481400-99484200	Weak transcription	Brain Substantia Nigra	brain
26	chr4:99481400-99485400	Weak transcription	Fetal Brain Male	brain
27	chr4:99481400-99485600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:99481400-99486000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:99481400-99486000	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:99481800-99483400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:99481800-99485200	Weak transcription	Brain Anterior Caudate	brain
32	chr4:99481800-99485400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:99481800-99485600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:99481800-99485600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:99481800-99485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:99481800-99486800	Weak transcription	HSMM	muscle
37	chr4:99482000-99485200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:99482200-99483600	Enhancers	NHEK	skin
39	chr4:99482200-99485200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:99482200-99485600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:99482200-99486000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:99482200-99486000	Weak transcription	Fetal Brain Female	brain
43	chr4:99482200-99486200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:99482400-99483400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr4:99482600-99483400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:99482600-99484200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:99482800-99483400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:99482800-99483400	Enhancers	Fetal Heart	heart
49	chr4:99482800-99484000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:99482800-99484200	Enhancers	HMEC	breast

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