Variant report

Variant	rs56680148
Chromosome Location	chr18:39620950-39620951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10502776	0.85[ASN][1000 genomes]
rs11082256	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12605021	0.85[ASN][1000 genomes]
rs12606434	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12607810	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12953847	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12954899	0.86[EUR][1000 genomes]
rs12956553	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12957030	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12959405	0.83[EUR][1000 genomes]
rs12961563	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12962602	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12962732	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544260	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16960213	0.85[ASN][1000 genomes]
rs16975459	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975462	0.84[ASN][1000 genomes]
rs28438873	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28541909	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28566843	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28708684	0.85[ASN][1000 genomes]
rs35269653	0.88[EUR][1000 genomes]
rs3813065	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819162	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4283305	0.83[EUR][1000 genomes]
rs4513183	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55971157	0.84[ASN][1000 genomes]
rs61682064	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62082284	0.81[EUR][1000 genomes]
rs62082292	0.88[EUR][1000 genomes]
rs62082876	0.85[EUR][1000 genomes]
rs7230624	0.93[ASN][1000 genomes]
rs7230883	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7233661	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237737	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237780	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237783	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7238178	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7239652	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7240218	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7241401	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7242727	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73454598	0.84[ASN][1000 genomes]
rs8087875	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8092954	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8095411	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9646518	0.81[EUR][1000 genomes]
rs9949409	0.85[ASN][1000 genomes]
rs9949895	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954624	0.84[ASN][1000 genomes]
rs9956832	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9958749	0.85[ASN][1000 genomes]
rs9964331	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9965466	0.84[ASN][1000 genomes]
rs9966146	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
5	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
6	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
7	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
9	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
10	chr18:39585400-39627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr18:39585600-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
13	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
14	chr18:39592200-39629400	Weak transcription	Fetal Brain Female	brain
15	chr18:39594600-39638800	Weak transcription	K562	blood
16	chr18:39597400-39622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
18	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr18:39606200-39628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:39607400-39626000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:39607600-39634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr18:39608600-39627400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr18:39608800-39631400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr18:39609000-39625600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr18:39609000-39628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr18:39609200-39624000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:39609200-39624200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr18:39609200-39625800	Strong transcription	Primary T cells from cord blood	blood
29	chr18:39609200-39626000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr18:39609200-39626600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr18:39609200-39631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr18:39609200-39631600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr18:39609400-39626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr18:39609800-39621800	Strong transcription	Placenta	Placenta
35	chr18:39609800-39622000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr18:39609800-39630400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:39610200-39621400	Strong transcription	GM12878-XiMat	blood
38	chr18:39610200-39626200	Strong transcription	Liver	Liver
39	chr18:39610600-39628000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr18:39611600-39627600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr18:39612200-39623000	Weak transcription	Fetal Intestine Small	intestine
42	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
43	chr18:39612200-39666400	Weak transcription	Gastric	stomach
44	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
45	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr18:39612400-39624000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr18:39613200-39622400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr18:39613400-39626200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr18:39613800-39631200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr18:39613800-39631400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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