Variant report

Variant	rs13065075
Chromosome Location	chr3:142265166-142265167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10935461	0.86[CHB][hapmap]
rs10935465	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129393	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061823	0.91[CHB][hapmap]
rs13067795	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13069307	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13075471	0.81[ASN][1000 genomes]
rs13085998	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13093869	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13098343	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1357530	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1916639	0.81[EUR][1000 genomes]
rs1983434	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1983435	0.82[EUR][1000 genomes]
rs2030613	0.86[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2049325	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2049326	0.82[EUR][1000 genomes]
rs2140432	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2177396	0.82[EUR][1000 genomes]
rs2227928	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227930	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354860	0.81[EUR][1000 genomes]
rs28617475	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2862743	0.91[CHB][hapmap]
rs2862745	0.91[CHB][hapmap]
rs3816805	0.86[CHB][hapmap]
rs3922730	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4273389	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4413348	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs4441672	0.92[CHB][hapmap]
rs4597728	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414350	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440078	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs6440082	0.91[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6440086	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440087	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440088	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440089	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440090	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440091	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440092	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440093	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440094	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440098	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6440099	0.82[EUR][1000 genomes]
rs6768093	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769786	0.92[CHB][hapmap]
rs6770155	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6772400	0.92[CHB][hapmap]
rs6775583	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775718	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6775813	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6780250	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782400	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783203	0.82[EUR][1000 genomes]
rs6784089	0.82[EUR][1000 genomes]
rs6785675	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6791816	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792259	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799752	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6802631	0.87[CHB][hapmap]
rs7428496	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610557	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7615316	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs7623524	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630130	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631313	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7634158	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7635146	0.81[EUR][1000 genomes]
rs7641330	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.82[EUR][1000 genomes]
rs7647573	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7651071	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651542	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9683085	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808914	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808943	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816736	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9820353	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820770	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824176	0.80[EUR][1000 genomes]
rs9824893	0.82[EUR][1000 genomes]
rs9825207	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826786	0.86[CHB][hapmap]
rs9828178	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap]
rs9855140	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9855919	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862919	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs9866958	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9869842	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876254	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9879995	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882763	0.82[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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
3	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
5	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
6	chr3:142209400-142271800	Weak transcription	HepG2	liver
7	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
8	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
9	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
11	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
12	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
13	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:142242400-142275800	Weak transcription	NHEK	skin
16	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
17	chr3:142248400-142269000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:142251800-142270800	Weak transcription	Fetal Kidney	kidney
21	chr3:142251800-142271600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:142253200-142269600	Weak transcription	Pancreas	Pancrea
23	chr3:142253200-142271200	Weak transcription	Psoas Muscle	Psoas
24	chr3:142253200-142271800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:142253400-142268000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:142253400-142268400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:142253400-142270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:142253400-142270600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:142253400-142270800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
32	chr3:142253600-142267600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:142253600-142268400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:142253600-142271600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:142254000-142270000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:142254200-142265400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:142254200-142268400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:142255000-142268400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:142255400-142265400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:142255400-142268000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:142255400-142268800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:142255600-142265400	Weak transcription	HSMM	muscle
44	chr3:142255600-142266000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:142255600-142268000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:142255600-142268600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:142255600-142269000	Weak transcription	Fetal Stomach	stomach
48	chr3:142255600-142269000	Weak transcription	Lung	lung
49	chr3:142255600-142269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:142255600-142270000	Weak transcription	Brain Hippocampus Middle	brain

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