Variant report

Variant	rs9798898
Chromosome Location	chr3:160082154-160082155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10212236	0.82[ASN][1000 genomes]
rs10513551	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918749	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13403	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451761	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451762	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1551190	0.86[AMR][1000 genomes]
rs1953506	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2152425	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279457	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305407	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773372	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3851366	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4091703	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272947	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679881	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679885	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679888	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4679889	0.82[ASN][1000 genomes]
rs4679891	0.85[AMR][1000 genomes]
rs4680576	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680580	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680585	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680587	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680588	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55687857	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55731730	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56197102	0.82[AMR][1000 genomes]
rs56394279	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58322641	0.82[ASN][1000 genomes]
rs58665246	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60009222	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60460891	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272186	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272791	0.85[AMR][1000 genomes]
rs62272792	0.81[AMR][1000 genomes]
rs62272794	0.81[AMR][1000 genomes]
rs6441313	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441314	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441319	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441320	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6791261	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792612	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793560	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6798668	0.83[EUR][1000 genomes]
rs6803828	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808083	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs721023	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73154592	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7356111	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611130	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618974	0.80[AMR][1000 genomes]
rs7621724	0.84[AMR][1000 genomes]
rs7624902	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7627749	0.82[ASN][1000 genomes]
rs7627756	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7629	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629202	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631792	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634108	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634826	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7640072	0.81[AMR][1000 genomes]
rs7645832	0.82[AMR][1000 genomes]
rs7647873	0.85[AMR][1000 genomes]
rs869468	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9799314	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9968151	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9798898	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:160049400-160090600	Weak transcription	NH-A	brain
3	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
9	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
10	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:160058400-160088800	Weak transcription	Osteobl	bone
14	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
15	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
16	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
17	chr3:160065000-160082800	Weak transcription	NHDF-Ad	bronchial
18	chr3:160065000-160091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:160066200-160086000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:160066400-160099200	Weak transcription	NHEK	skin
21	chr3:160066800-160083200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:160068600-160086000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:160068600-160096000	Weak transcription	Gastric	stomach
25	chr3:160068800-160094000	Weak transcription	Adipose Nuclei	Adipose
26	chr3:160068800-160094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:160069800-160087600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:160070200-160086200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:160070400-160092400	Weak transcription	HMEC	breast
31	chr3:160070600-160085800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:160071000-160091000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:160071400-160083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:160071400-160098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
36	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
37	chr3:160071800-160091800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:160071800-160092000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:160072000-160096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:160072600-160086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:160072600-160096200	Weak transcription	HepG2	liver
42	chr3:160072800-160087400	Weak transcription	Brain Substantia Nigra	brain
43	chr3:160072800-160091200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:160073000-160091600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:160073000-160092600	Weak transcription	Fetal Kidney	kidney
46	chr3:160073200-160091600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:160073200-160097200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:160073400-160088800	Weak transcription	Fetal Stomach	stomach
49	chr3:160073400-160090800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr3:160073400-160099200	Weak transcription	HSMMtube	muscle

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