Variant report

Variant	rs11489073
Chromosome Location	chr3:112330056-112330057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11706550	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1512005	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1512006	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1877363	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1994713	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101632	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131008	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2172196	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279532	0.82[EUR][1000 genomes]
rs2280066	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2464611	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638016	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638017	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638018	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638022	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638031	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638037	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638042	0.92[EUR][1000 genomes]
rs2638045	0.90[EUR][1000 genomes]
rs2668217	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2668220	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2668222	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2668223	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705517	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705543	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28866814	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2933142	0.94[EUR][1000 genomes]
rs2952326	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2952327	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34233684	0.82[EUR][1000 genomes]
rs3732815	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5000995	0.82[EUR][1000 genomes]
rs7652377	0.82[EUR][1000 genomes]
rs766968	0.82[EUR][1000 genomes]
rs9288954	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866734	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9869455	0.82[EUR][1000 genomes]
rs9869579	0.82[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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11489073	SLC35A5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
3	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:112300200-112331000	Weak transcription	Lung	lung
6	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
7	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
9	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
11	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
15	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:112316400-112333600	Weak transcription	A549	lung
17	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:112318200-112330600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:112322200-112337200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:112323400-112332400	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr3:112323800-112334600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:112324400-112331200	Strong transcription	Adipose Nuclei	Adipose
24	chr3:112324600-112331800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:112324800-112330600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:112325600-112330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:112326000-112333400	Weak transcription	Ovary	ovary
28	chr3:112327200-112330600	Weak transcription	Fetal Heart	heart
29	chr3:112327200-112331200	Weak transcription	HUVEC	blood vessel
30	chr3:112327200-112331600	Weak transcription	Fetal Lung	lung
31	chr3:112327600-112330400	Weak transcription	NHLF	lung
32	chr3:112327800-112330200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:112327800-112340600	Weak transcription	Fetal Kidney	kidney
34	chr3:112328200-112332200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:112328400-112332600	Genic enhancers	Osteobl	bone
36	chr3:112328600-112332600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:112329000-112331600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:112329000-112334400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:112329200-112330400	Weak transcription	NH-A	brain
40	chr3:112329200-112333400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:112329400-112330200	Weak transcription	HSMMtube	muscle
42	chr3:112329400-112330600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:112329400-112331200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:112329400-112333400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:112329400-112333400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:112329400-112334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:112329600-112331000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:112329600-112341800	Strong transcription	HSMM	muscle
49	chr3:112329800-112331400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:112330000-112330600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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