Variant report

Variant	rs3749482
Chromosome Location	chr4:79465559-79465560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79464026..79467254-chr4:79471898..79474362,3	MCF-7	breast:
2	chr4:79463978..79466119-chr4:79474806..79476481,2	K562	blood:
3	chr4:79463825..79467444-chr4:79478158..79482300,4	MCF-7	breast:
4	chr4:79463304..79464850-chr4:79465136..79467888,2	K562	blood:

Variant related genes	Relation type
ENSG00000138772	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11098227	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11098228	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098229	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11936220	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940309	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13137102	0.86[EUR][1000 genomes]
rs13142813	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17003337	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17003342	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34970825	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36039411	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749485	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3811747	1.00[ASW][hapmap];0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975143	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975144	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66676781	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67325389	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9760192	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9761952	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3749482	ANXA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
2	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
4	chr4:79428200-79466200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:79435600-79467200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:79440600-79465800	Weak transcription	Lung	lung
7	chr4:79440600-79467200	Weak transcription	Left Ventricle	heart
8	chr4:79442400-79465600	Weak transcription	Fetal Stomach	stomach
9	chr4:79444800-79472400	Weak transcription	Right Atrium	heart
10	chr4:79453400-79467200	Weak transcription	Placenta	Placenta
11	chr4:79456400-79471200	Weak transcription	Fetal Kidney	kidney
12	chr4:79457000-79471200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:79458600-79471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:79461800-79466000	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:79462200-79467200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:79462200-79468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:79462600-79467800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:79463000-79466000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:79463000-79466200	Enhancers	Fetal Heart	heart
20	chr4:79463000-79467600	Enhancers	HMEC	breast
21	chr4:79463000-79468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:79463000-79468400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:79463000-79472200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:79463200-79465600	Enhancers	Osteobl	bone
25	chr4:79463200-79466400	Weak transcription	HepG2	liver
26	chr4:79463200-79467600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:79463200-79470800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:79463400-79467800	Enhancers	NHDF-Ad	bronchial
29	chr4:79463400-79467800	Enhancers	NHLF	lung
30	chr4:79463400-79468000	Enhancers	Hela-S3	cervix
31	chr4:79463600-79466600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:79463600-79471200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:79463600-79472600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:79463800-79466800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:79463800-79471800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:79464200-79466000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:79464200-79466200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:79464200-79466200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:79464200-79466200	Enhancers	Fetal Intestine Large	intestine
40	chr4:79464200-79466400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:79464200-79466600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:79464200-79466600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:79464200-79467400	Enhancers	A549	lung
44	chr4:79464200-79467600	Enhancers	Fetal Lung	lung
45	chr4:79464200-79469800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:79464600-79466400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:79464600-79467600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:79464800-79467200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:79464800-79467200	Weak transcription	Pancreas	Pancrea
50	chr4:79464800-79471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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