Variant report

Variant	rs17304079
Chromosome Location	chr3:50085153-50085154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1046956	1.00[ASN][1000 genomes]
rs1061474	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs1138536	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs11709573	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs12637671	1.00[CHD][hapmap];0.91[MEX][hapmap]
rs13059311	1.00[ASN][1000 genomes]
rs13064381	1.00[ASN][1000 genomes]
rs13067082	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs13071931	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097720	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14321	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17657664	0.83[LWK][hapmap];0.94[YRI][hapmap]
rs1799844	1.00[ASN][1000 genomes]
rs2014004	0.88[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189691	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2526384	1.00[ASN][1000 genomes]
rs2526387	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526397	1.00[CHD][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs2526398	1.00[ASN][1000 genomes]
rs2526747	0.91[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2624815	0.80[AFR][1000 genomes]
rs2624826	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs2624833	1.00[ASN][1000 genomes]
rs2624841	1.00[ASN][1000 genomes]
rs2624846	0.82[EUR][1000 genomes]
rs35012435	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35129566	1.00[ASN][1000 genomes]
rs35375092	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774734	0.91[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs3774759	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs55924524	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58339610	1.00[ASN][1000 genomes]
rs62260663	1.00[ASN][1000 genomes]
rs62260720	1.00[ASN][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262118	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	1.00[ASN][1000 genomes]
rs62263602	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762477	0.91[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6785500	0.81[YRI][hapmap]
rs6787892	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804970	1.00[ASN][1000 genomes]
rs7061	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs71326904	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71326915	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613603	1.00[ASN][1000 genomes]
rs7615206	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs7615318	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7620848	1.00[ASN][1000 genomes]
rs7621797	1.00[ASN][1000 genomes]
rs7627864	1.00[YRI][hapmap]
rs7635601	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637711	1.00[ASN][1000 genomes]
rs7648652	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	1.00[ASN][1000 genomes]
rs868891	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs9682295	0.85[AFR][1000 genomes]
rs9829155	1.00[ASN][1000 genomes]
rs9835157	1.00[ASN][1000 genomes]
rs9836756	1.00[ASN][1000 genomes]
rs9851651	1.00[ASN][1000 genomes]
rs9858297	1.00[ASN][1000 genomes]
rs9870755	1.00[ASN][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	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17304079	RNF123	cis	parietal	SCAN
rs17304079	QARS	cis	parietal	SCAN
rs17304079	RBM6	cis	Whole Blood	GTEx
rs17304079	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs17304079	GNL3	cis	parietal	SCAN
rs17304079	ARIH2	cis	cerebellum	SCAN
rs17304079	RBM6	cis	Artery Tibial	GTEx
rs17304079	ITIH3	cis	cerebellum	SCAN
rs17304079	QRICH1	cis	cerebellum	SCAN
rs17304079	RBM6	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50010800-50087000	Weak transcription	NHLF	lung
2	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
3	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
5	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
11	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:50046800-50085800	Weak transcription	HMEC	breast
13	chr3:50047200-50085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:50047200-50085400	Weak transcription	Left Ventricle	heart
15	chr3:50047200-50092600	Weak transcription	Gastric	stomach
16	chr3:50048800-50085600	Weak transcription	A549	lung
17	chr3:50051600-50095200	Weak transcription	Pancreas	Pancrea
18	chr3:50051800-50085400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:50052200-50087000	Weak transcription	NHDF-Ad	bronchial
20	chr3:50052400-50085600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:50055600-50085600	Weak transcription	Hela-S3	cervix
22	chr3:50056400-50114400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:50057000-50085400	Weak transcription	Fetal Lung	lung
24	chr3:50057200-50085200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:50057200-50085400	Weak transcription	NHEK	skin
26	chr3:50058400-50085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:50058600-50085200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:50058800-50085400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:50062000-50091400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:50062200-50093400	Weak transcription	Small Intestine	intestine
31	chr3:50066000-50085400	Weak transcription	Fetal Kidney	kidney
32	chr3:50066000-50085600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:50066400-50085600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:50066600-50086800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:50066800-50087400	Weak transcription	NH-A	brain
36	chr3:50071800-50087600	Weak transcription	HSMMtube	muscle
37	chr3:50072200-50085600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:50072800-50085200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:50072800-50095200	Weak transcription	Fetal Heart	heart
40	chr3:50077600-50085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:50078400-50102400	Weak transcription	Psoas Muscle	Psoas
42	chr3:50078600-50085200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:50078800-50085200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:50078800-50092000	Weak transcription	Ovary	ovary
45	chr3:50079000-50085200	Weak transcription	HepG2	liver
46	chr3:50079000-50085800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:50079200-50085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:50079200-50085400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:50079200-50087400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:50079200-50095200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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