Variant report

Variant	rs9311485
Chromosome Location	chr3:52987645-52987646
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11130331	0.83[GIH][hapmap]
rs11130332	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11706243	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11707576	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708223	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072536	0.80[CEU][hapmap]
rs13082061	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13083728	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1573815	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs17304995	1.00[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2245424	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2246556	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs2257216	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs2276817	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2276825	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs2336162	0.90[EUR][1000 genomes]
rs2336666	0.83[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336670	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2336671	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2336672	0.81[ASN][1000 genomes]
rs2564930	0.80[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581779	0.92[EUR][1000 genomes]
rs2581780	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs2581796	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2581797	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581801	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581802	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581803	0.95[JPT][hapmap]
rs2581805	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2581815	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2581819	0.80[ASN][1000 genomes]
rs2581820	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581823	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710314	0.91[JPT][hapmap]
rs2710326	0.82[ASN][1000 genomes]
rs2710342	0.84[EUR][1000 genomes]
rs2710345	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710346	0.80[ASN][1000 genomes]
rs34230854	0.86[EUR][1000 genomes]
rs35380116	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733047	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4302374	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4515041	0.82[ASN][1000 genomes]
rs4519686	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687554	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4687559	0.84[EUR][1000 genomes]
rs4687560	0.84[EUR][1000 genomes]
rs4687658	0.82[CEU][hapmap]
rs4687663	0.82[CEU][hapmap]
rs4687672	0.81[CEU][hapmap]
rs4687687	0.83[GIH][hapmap]
rs4687692	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59989280	0.85[EUR][1000 genomes]
rs6445538	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6445539	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6445547	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6770957	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6773040	0.85[EUR][1000 genomes]
rs6789219	0.85[EUR][1000 genomes]
rs6792578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797399	0.82[EUR][1000 genomes]
rs6803519	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6805298	0.85[EUR][1000 genomes]
rs71301803	0.86[EUR][1000 genomes]
rs71301807	0.88[EUR][1000 genomes]
rs7621939	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7644973	0.88[EUR][1000 genomes]
rs7648514	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652131	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9682464	0.94[CEU][hapmap]
rs9812543	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9813024	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9823697	0.91[JPT][hapmap]
rs9825679	0.85[ASN][1000 genomes]
rs9828491	0.83[EUR][1000 genomes]
rs9831409	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9839035	0.82[EUR][1000 genomes]
rs9842974	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9844736	1.00[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9846976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9847024	0.92[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];0.93[TSI][hapmap];0.86[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	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9311485	RBM6	cis	cerebellum	SCAN
rs9311485	ITIH4-AS1	cis	lung	GTEx
rs9311485	SEMA3G	cis	parietal	SCAN
rs9311485	MUSTN1	cis	Artery Aorta	GTEx
rs9311485	SERBP1P3	cis	lung	GTEx
rs9311485	WDR6	cis	cerebellum	SCAN
rs9311485	AMT	cis	parietal	SCAN
rs9311485	GNL3	cis	cerebellum	SCAN
rs9311485	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9311485	ITIH4	cis	lymphoblastoid	seeQTL
rs9311485	TMEM110	cis	parietal	SCAN
rs9311485	GNL3	cis	parietal	SCAN
rs9311485	CHDH	cis	parietal	SCAN
rs9311485	RFT1	cis	cerebellum	SCAN
rs9311485	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9311485	ITIH4	cis	parietal	SCAN
rs9311485	ITIH4	cis	cerebellum	SCAN
rs9311485	NT5DC2	cis	parietal	SCAN
rs9311485	TMEM110	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52962400-52998200	Weak transcription	Lung	lung
4	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:52964200-52995400	Weak transcription	Gastric	stomach
8	chr3:52964400-52988200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:52965000-52998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
12	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
13	chr3:52966400-53001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:52969200-52991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:52969200-52996200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:52969200-52997400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:52975200-53000600	Weak transcription	Hela-S3	cervix
20	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:52980400-52996600	Weak transcription	Psoas Muscle	Psoas
22	chr3:52980800-52990000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52983600-52988200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:52984000-52998800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:52984400-52988200	Strong transcription	Fetal Stomach	stomach
26	chr3:52984400-53006000	Weak transcription	Fetal Heart	heart
27	chr3:52984600-53003000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:52985000-52988000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:52985200-52988400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52986000-52987800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52986000-52987800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:52986000-52987800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52986000-52988000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:52986000-52988200	Strong transcription	Dnd41	blood
35	chr3:52986200-52987800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:52986200-52993800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:52986400-52987800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:52986400-52987800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:52986400-52988000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:52986400-52988000	Strong transcription	Primary T cells from cord blood	blood
41	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:52986600-52988000	Strong transcription	Fetal Intestine Small	intestine
43	chr3:52986800-52989200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:52986800-52993000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:52986800-52999000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:52986800-53001600	Weak transcription	Liver	Liver
47	chr3:52986800-53006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:52987000-52987800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:52987000-52991400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:52987000-53002000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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