Variant report

Variant	rs6440089
Chromosome Location	chr3:142279796-142279797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10935465	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925693	0.93[CHD][hapmap];0.82[GIH][hapmap]
rs13061823	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs13065075	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13067795	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069307	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13079246	0.81[CEU][hapmap]
rs13085998	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13093869	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098343	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357529	0.84[EUR][1000 genomes]
rs1357530	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs16852486	0.81[CEU][hapmap]
rs1916639	0.85[EUR][1000 genomes]
rs1983434	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1983435	0.86[EUR][1000 genomes]
rs2030613	0.92[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2049325	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2049326	0.86[EUR][1000 genomes]
rs2140432	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2177396	0.86[EUR][1000 genomes]
rs2227928	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227930	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354860	0.85[EUR][1000 genomes]
rs28617475	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2862743	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs2883380	0.81[CEU][hapmap]
rs3922730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs4273389	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413348	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs4441672	0.91[CHB][hapmap]
rs4597728	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683690	0.81[CEU][hapmap]
rs6414350	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440082	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[YRI][hapmap]
rs6440086	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440087	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440090	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440091	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440092	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440093	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440098	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs6440099	0.86[EUR][1000 genomes]
rs6768093	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769786	0.91[CHB][hapmap]
rs6770155	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6772400	0.91[CHB][hapmap]
rs6775583	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775718	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775813	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6780250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6783203	0.86[EUR][1000 genomes]
rs6784089	0.86[EUR][1000 genomes]
rs6785675	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6789958	0.80[CEU][hapmap]
rs6791816	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6793735	0.81[CEU][hapmap]
rs6798232	0.81[CEU][hapmap]
rs6799752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802631	0.86[CHB][hapmap]
rs6802734	0.81[EUR][1000 genomes]
rs6802774	0.82[EUR][1000 genomes]
rs6808205	0.81[CEU][hapmap]
rs7428496	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7430429	0.81[CEU][hapmap]
rs7609842	0.80[EUR][1000 genomes]
rs7610557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7615316	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7623524	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630130	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631313	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7634158	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7635146	0.85[EUR][1000 genomes]
rs7641330	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646880	0.86[EUR][1000 genomes]
rs7647573	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651542	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652687	0.91[CHD][hapmap]
rs9683085	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9808914	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9808943	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816736	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9820353	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9820770	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9824176	0.80[EUR][1000 genomes]
rs9824893	0.86[EUR][1000 genomes]
rs9825207	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826786	0.86[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap]
rs9828178	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9832606	0.81[CEU][hapmap]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs9855140	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9855919	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862919	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs9866958	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs9869842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876254	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9879995	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882763	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6440089	XRN1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
3	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
4	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
5	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
7	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:142256200-142283600	Weak transcription	Aorta	Aorta
12	chr3:142259800-142285600	Strong transcription	Dnd41	blood
13	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:142263400-142286200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:142263600-142288000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:142263800-142285600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:142263800-142286600	Strong transcription	Liver	Liver
18	chr3:142264000-142285200	Strong transcription	Fetal Thymus	thymus
19	chr3:142265200-142285000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:142265200-142287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:142265400-142283600	Weak transcription	HSMMtube	muscle
22	chr3:142266400-142285600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:142267000-142286600	Strong transcription	Primary B cells from cord blood	blood
24	chr3:142267600-142282000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:142267800-142285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:142268800-142284200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:142269200-142292600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:142270000-142287200	Weak transcription	Pancreas	Pancrea
29	chr3:142270200-142285000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:142270800-142285200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:142270800-142286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:142271000-142285400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:142271800-142282200	Weak transcription	Fetal Kidney	kidney
34	chr3:142271800-142285200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:142272200-142286200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:142272400-142282200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:142272600-142279800	Weak transcription	Fetal Lung	lung
38	chr3:142272600-142280200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:142272600-142282000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:142272600-142283600	Weak transcription	Fetal Brain Female	brain
41	chr3:142272600-142284800	Weak transcription	HepG2	liver
42	chr3:142272600-142287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:142272600-142296200	Weak transcription	Brain Angular Gyrus	brain
44	chr3:142272600-142296200	Weak transcription	Psoas Muscle	Psoas
45	chr3:142272800-142293400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:142274000-142284800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:142274000-142285200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:142274000-142286600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:142274000-142287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:142274000-142287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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