Variant report

Variant	rs12456573
Chromosome Location	chr18:39620376-39620377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10221315	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10468957	0.86[EUR][1000 genomes]
rs10775471	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11082255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11082257	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12326267	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12455038	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12455083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12455780	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12456084	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12456761	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12456934	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12457082	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12457086	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12457354	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12457525	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12964834	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12964931	0.86[EUR][1000 genomes]
rs12966303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13381503	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1368025	0.89[EUR][1000 genomes]
rs1432138	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1557418	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1573497	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16975431	0.87[EUR][1000 genomes]
rs16975474	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1897396	0.87[EUR][1000 genomes]
rs1897397	0.87[EUR][1000 genomes]
rs1941526	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1941532	0.85[EUR][1000 genomes]
rs1942151	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1942152	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1984366	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984367	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043220	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2156015	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2334943	0.87[EUR][1000 genomes]
rs34966612	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4121647	0.81[AMR][1000 genomes]
rs4890221	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4890377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890378	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4890379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5004531	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs510946	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56147258	0.85[EUR][1000 genomes]
rs56211042	0.80[AMR][1000 genomes]
rs569983	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57794431	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs581950	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60861018	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61107251	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62082282	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62082880	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62082911	0.85[EUR][1000 genomes]
rs627099	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs639660	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650586	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6507451	0.89[EUR][1000 genomes]
rs657164	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs667503	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66960332	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7237459	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7239288	0.86[EUR][1000 genomes]
rs7241193	0.87[EUR][1000 genomes]
rs7504589	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8093251	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304263	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs948873	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9635942	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9807114	0.86[EUR][1000 genomes]
rs9807279	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9807400	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9807487	0.87[EUR][1000 genomes]
rs9948913	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9989595	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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:123 , 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	chr18:39602200-39620800	Weak transcription	A549	lung
20	chr18:39605600-39620400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr18:39606200-39628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr18:39607400-39626000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr18:39607600-39634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr18:39608600-39627400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr18:39608800-39631400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr18:39609000-39625600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr18:39609000-39628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr18:39609200-39624000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:39609200-39624200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:39609200-39625800	Strong transcription	Primary T cells from cord blood	blood
31	chr18:39609200-39626000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:39609200-39626600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr18:39609200-39631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:39609200-39631600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr18:39609400-39626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr18:39609800-39621800	Strong transcription	Placenta	Placenta
37	chr18:39609800-39622000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr18:39609800-39630400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr18:39610200-39621400	Strong transcription	GM12878-XiMat	blood
40	chr18:39610200-39626200	Strong transcription	Liver	Liver
41	chr18:39610600-39628000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr18:39611600-39627600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:39612200-39623000	Weak transcription	Fetal Intestine Small	intestine
44	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
45	chr18:39612200-39666400	Weak transcription	Gastric	stomach
46	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
47	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:39612400-39624000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr18:39613200-39622400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr18:39613400-39626200	Strong transcription	Duodenum Mucosa	Duodenum

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