Variant report

Variant	rs6440088
Chromosome Location	chr3:142270359-142270360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10935465	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1129393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065075	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13067795	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13069307	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13085998	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093869	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13098343	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1357529	0.84[EUR][1000 genomes]
rs1357530	0.85[EUR][1000 genomes]
rs1916639	0.85[EUR][1000 genomes]
rs1983434	0.86[EUR][1000 genomes]
rs1983435	0.86[EUR][1000 genomes]
rs2030613	0.86[EUR][1000 genomes]
rs2049325	0.86[EUR][1000 genomes]
rs2049326	0.86[EUR][1000 genomes]
rs2140432	0.86[EUR][1000 genomes]
rs2177396	0.86[EUR][1000 genomes]
rs2227928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2354860	0.85[EUR][1000 genomes]
rs28617475	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3922730	0.88[EUR][1000 genomes]
rs4273389	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4413348	0.86[EUR][1000 genomes]
rs4597728	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6414350	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440086	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440089	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];0.86[ASN][1000 genomes]
rs6440091	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440092	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440093	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440094	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440098	0.85[EUR][1000 genomes]
rs6440099	0.86[EUR][1000 genomes]
rs6768093	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6770155	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6775583	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6775718	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775813	0.86[EUR][1000 genomes]
rs6780250	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6782400	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6783203	0.86[EUR][1000 genomes]
rs6784089	0.86[EUR][1000 genomes]
rs6785675	0.88[EUR][1000 genomes]
rs6791816	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792259	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6799752	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6802734	0.81[EUR][1000 genomes]
rs6802774	0.82[EUR][1000 genomes]
rs7428496	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609842	0.80[EUR][1000 genomes]
rs7610557	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7615316	0.86[EUR][1000 genomes]
rs7623524	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7630130	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631313	0.85[EUR][1000 genomes]
rs7634158	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7635146	0.85[EUR][1000 genomes]
rs7641330	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646880	0.86[EUR][1000 genomes]
rs7647573	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651071	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651542	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9683085	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9808914	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9808943	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816736	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9820353	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9820770	0.86[EUR][1000 genomes];0.80[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];0.93[ASN][1000 genomes]
rs9828178	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9846960	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855140	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9855919	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9866958	0.85[EUR][1000 genomes]
rs9869842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876254	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879995	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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

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	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
11	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:142241800-142270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:142242400-142275800	Weak transcription	NHEK	skin
14	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
15	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:142248600-142273600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:142251800-142270800	Weak transcription	Fetal Kidney	kidney
18	chr3:142251800-142271600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:142253200-142271200	Weak transcription	Psoas Muscle	Psoas
20	chr3:142253200-142271800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:142253400-142270600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:142253400-142270800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:142253600-142271600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:142255600-142270600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:142255600-142270800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:142255600-142271400	Weak transcription	Ovary	ovary
30	chr3:142255600-142273800	Weak transcription	Gastric	stomach
31	chr3:142255600-142274200	Weak transcription	NHLF	lung
32	chr3:142255800-142270600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:142256200-142283600	Weak transcription	Aorta	Aorta
34	chr3:142257200-142274200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:142259800-142285600	Strong transcription	Dnd41	blood
36	chr3:142262400-142271000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:142262400-142271800	Weak transcription	Osteobl	bone
38	chr3:142263000-142270600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:142263200-142273800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:142263400-142286200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:142263600-142272600	Strong transcription	Adipose Nuclei	Adipose
43	chr3:142263600-142288000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:142263800-142272800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:142263800-142285600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:142263800-142286600	Strong transcription	Liver	Liver
47	chr3:142264000-142270600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:142264000-142279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:142264000-142285200	Strong transcription	Fetal Thymus	thymus
50	chr3:142265200-142276600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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