Variant report

Variant	rs6532748
Chromosome Location	chr4:99468567-99468568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10018825	0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs10021296	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11730384	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13114571	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13132635	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13134231	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs13149070	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs1573478	0.81[CEU][hapmap]
rs1919210	0.91[EUR][1000 genomes]
rs1919211	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866017	0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs4699345	0.96[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4699346	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4699646	0.88[EUR][1000 genomes]
rs4699648	0.91[EUR][1000 genomes]
rs4699650	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4699651	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4699652	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6532742	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6532744	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6532745	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6532747	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6823547	0.91[EUR][1000 genomes]
rs6827510	0.82[ASN][1000 genomes]
rs6831464	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6831643	0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6837359	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6846287	0.82[ASN][1000 genomes]
rs6854339	0.82[ASN][1000 genomes]
rs7658853	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7672134	0.94[JPT][hapmap];0.81[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6532748	TSPAN5	cis	cerebellum	SCAN
rs6532748	H2AFZ	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99459200-99479600	Weak transcription	Spleen	Spleen
2	chr4:99463800-99478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:99466400-99477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:99466600-99479800	Weak transcription	Fetal Thymus	thymus
5	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:99467600-99468600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr4:99467600-99468800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:99467600-99468800	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:99467800-99468600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:99467800-99468600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:99467800-99468600	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr4:99467800-99468600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:99467800-99468600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr4:99467800-99468600	Active TSS	Right Atrium	heart
15	chr4:99467800-99468600	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr4:99467800-99468600	Active TSS	HSMMtube	muscle
17	chr4:99467800-99468800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:99467800-99468800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr4:99467800-99468800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:99467800-99468800	Active TSS	Aorta	Aorta
21	chr4:99467800-99468800	Active TSS	Brain Angular Gyrus	brain
22	chr4:99467800-99468800	Active TSS	Brain Anterior Caudate	brain
23	chr4:99467800-99468800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr4:99467800-99468800	Flanking Active TSS	Fetal Brain Female	brain
25	chr4:99467800-99468800	Active TSS	Ovary	ovary
26	chr4:99467800-99468800	Active TSS	NHLF	lung
27	chr4:99467800-99469000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:99468000-99468600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:99468000-99468600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:99468000-99468600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:99468000-99468600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr4:99468000-99468600	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr4:99468000-99468600	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr4:99468000-99468600	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr4:99468000-99468600	Flanking Active TSS	Fetal Stomach	stomach
36	chr4:99468000-99468600	Active TSS	Psoas Muscle	Psoas
37	chr4:99468000-99468600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr4:99468000-99468800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:99468000-99468800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:99468000-99468800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:99468000-99468800	Active TSS	Brain Cingulate Gyrus	brain
42	chr4:99468000-99468800	Active TSS	Fetal Lung	lung
43	chr4:99468000-99468800	Flanking Active TSS	HUVEC	blood vessel
44	chr4:99468000-99468800	Flanking Active TSS	NH-A	brain
45	chr4:99468000-99468800	Active TSS	Osteobl	bone
46	chr4:99468200-99468600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:99468200-99468600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:99468200-99468600	Active TSS	Colonic Mucosa	Colon
49	chr4:99468200-99468800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:99468200-99468800	Active TSS	Rectal Smooth Muscle	rectum

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