Variant report

Variant	rs16975466
Chromosome Location	chr18:39552141-39552142
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:39535319..39538117-chr18:39550578..39552520,2	K562	blood:
2	chr18:39549732..39552143-chr18:39580474..39582675,2	K562	blood:
3	chr18:39550418..39552768-chr18:39552800..39556152,4	K562	blood:
4	chr18:39551912..39556568-chr18:39556669..39562027,6	K562	blood:
5	chr18:39551994..39554075-chr18:39573084..39575388,2	K562	blood:
6	chr18:39551912..39554681-chr18:39556259..39560409,4	K562	blood:

Variant related genes	Relation type
ENSG00000078142	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1142044	1.00[EUR][1000 genomes]
rs11873469	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873602	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874766	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874775	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874814	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11874830	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11876578	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11877901	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1540057	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975441	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975447	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975463	1.00[EUR][1000 genomes]
rs16975521	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2469471	1.00[EUR][1000 genomes]
rs490578	1.00[EUR][1000 genomes]
rs493100	1.00[EUR][1000 genomes]
rs525369	1.00[EUR][1000 genomes]
rs542870	1.00[EUR][1000 genomes]
rs55655849	1.00[EUR][1000 genomes]
rs563840	1.00[EUR][1000 genomes]
rs56411890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56751463	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56979511	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57208863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575366	1.00[EUR][1000 genomes]
rs58298297	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs583163	1.00[EUR][1000 genomes]
rs58390786	1.00[EUR][1000 genomes]
rs584022	1.00[EUR][1000 genomes]
rs586797	1.00[EUR][1000 genomes]
rs58881642	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs591870	1.00[EUR][1000 genomes]
rs593689	1.00[EUR][1000 genomes]
rs606366	1.00[EUR][1000 genomes]
rs608428	1.00[EUR][1000 genomes]
rs61095714	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs616575	1.00[EUR][1000 genomes]
rs633541	1.00[EUR][1000 genomes]
rs635560	1.00[EUR][1000 genomes]
rs640064	1.00[EUR][1000 genomes]
rs640460	1.00[EUR][1000 genomes]
rs643772	1.00[EUR][1000 genomes]
rs645148	1.00[EUR][1000 genomes]
rs647084	1.00[EUR][1000 genomes]
rs6507453	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6507454	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs655693	1.00[EUR][1000 genomes]
rs659950	1.00[EUR][1000 genomes]
rs6650669	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs669235	1.00[EUR][1000 genomes]
rs670429	1.00[EUR][1000 genomes]
rs674380	1.00[EUR][1000 genomes]
rs684091	1.00[EUR][1000 genomes]
rs7229485	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237185	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7237815	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7238919	1.00[EUR][1000 genomes]
rs7239880	1.00[EUR][1000 genomes]
rs7240066	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7241399	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7242077	1.00[EUR][1000 genomes]
rs7245131	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7343027	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73448558	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73451096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73452235	1.00[EUR][1000 genomes]
rs73452297	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73452300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73453013	1.00[EUR][1000 genomes]
rs73454552	1.00[EUR][1000 genomes]
rs73454573	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454581	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454593	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454596	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73454602	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73950814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8084037	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8085708	1.00[EUR][1000 genomes]
rs8088187	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8089142	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8090403	1.00[EUR][1000 genomes]
rs8095945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9948650	1.00[EUR][1000 genomes]
rs9965647	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:121 , 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	chr18:39536200-39552400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:39536200-39564800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:39536200-39568600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:39536400-39552400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr18:39536400-39578200	Weak transcription	A549	lung
7	chr18:39536800-39580000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr18:39537400-39552400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:39537400-39553000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:39537400-39555800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr18:39537600-39552200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr18:39537600-39552800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr18:39537600-39553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr18:39542400-39552400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr18:39544400-39552200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:39545000-39552200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr18:39545000-39552400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr18:39545200-39555600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:39545600-39583600	Weak transcription	Small Intestine	intestine
21	chr18:39546000-39557400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:39546200-39563800	Weak transcription	Fetal Heart	heart
23	chr18:39547400-39564600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:39547600-39557400	Weak transcription	Fetal Intestine Small	intestine
25	chr18:39547600-39559200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:39547600-39580600	Weak transcription	Spleen	Spleen
27	chr18:39547800-39569000	Weak transcription	Fetal Brain Female	brain
28	chr18:39548000-39552200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr18:39548000-39553400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:39548000-39553400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr18:39548000-39554200	Weak transcription	Right Ventricle	heart
32	chr18:39548000-39557400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr18:39548000-39576000	Weak transcription	Fetal Brain Male	brain
34	chr18:39548000-39580200	Weak transcription	Pancreas	Pancrea
35	chr18:39548200-39552600	Weak transcription	Thymus	Thymus
36	chr18:39548200-39555000	Weak transcription	Aorta	Aorta
37	chr18:39548200-39557600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr18:39548200-39557600	Weak transcription	Fetal Stomach	stomach
39	chr18:39548200-39564600	Weak transcription	Esophagus	oesophagus
40	chr18:39548200-39564800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:39548200-39569200	Weak transcription	Ovary	ovary
42	chr18:39548200-39576600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr18:39548200-39579400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr18:39548200-39580200	Weak transcription	Lung	lung
45	chr18:39548200-39580400	Weak transcription	NHLF	lung
46	chr18:39548400-39552200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr18:39548400-39553800	Weak transcription	Colon Smooth Muscle	Colon
48	chr18:39548400-39557200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr18:39548400-39557600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:39548400-39562600	Weak transcription	NHEK	skin

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