Variant report

Variant	rs62082880
Chromosome Location	chr18:39655171-39655172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:39653176..39655902-chr18:39657058..39659990,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10221315	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10468957	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10775471	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11082255	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11082257	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12326267	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12455038	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12455083	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12455780	0.81[EUR][1000 genomes]
rs12456084	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12456573	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12456761	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12456934	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12457082	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12457086	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12457354	0.83[AMR][1000 genomes]
rs12457525	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12964834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964931	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12966303	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13381503	0.82[EUR][1000 genomes]
rs1368025	0.80[EUR][1000 genomes]
rs1432138	0.83[AMR][1000 genomes]
rs1557418	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1573497	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16975474	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1941526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941532	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1942151	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1942152	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1984366	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1984367	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2043220	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2156015	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34966612	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4121647	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4890221	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4890377	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4890378	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4890379	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5004531	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs510946	0.83[EUR][1000 genomes]
rs56147258	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56211042	0.82[AMR][1000 genomes]
rs569983	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57794431	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs581950	0.86[EUR][1000 genomes]
rs60861018	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61107251	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62082282	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62082911	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs627099	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639660	0.86[EUR][1000 genomes]
rs650586	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6507451	0.80[EUR][1000 genomes]
rs657164	0.81[EUR][1000 genomes]
rs667503	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66960332	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7237459	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7504589	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8093251	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304263	0.81[EUR][1000 genomes]
rs948873	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9635942	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9807114	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9807279	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9807400	0.83[AMR][1000 genomes]
rs9948913	0.81[EUR][1000 genomes]
rs9989595	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
6	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
7	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
8	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
9	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
10	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS 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	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 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	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
3	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
5	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
6	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:39612200-39666400	Weak transcription	Gastric	stomach
8	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
9	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr18:39619200-39656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:39619800-39662200	Weak transcription	Right Ventricle	heart
13	chr18:39620800-39664200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:39621200-39657200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:39628600-39666200	Weak transcription	A549	lung
16	chr18:39630600-39658600	Weak transcription	Hela-S3	cervix
17	chr18:39631200-39659800	Weak transcription	Fetal Brain Male	brain
18	chr18:39634800-39674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr18:39639400-39664000	Weak transcription	K562	blood
20	chr18:39644200-39674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:39644400-39656800	Weak transcription	HUVEC	blood vessel
22	chr18:39644600-39665000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr18:39644800-39660200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:39644800-39662800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr18:39644800-39664200	Strong transcription	Liver	Liver
26	chr18:39644800-39665000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr18:39645000-39664000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr18:39648000-39657400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr18:39648000-39661200	Weak transcription	HMEC	breast
30	chr18:39648200-39656400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr18:39648200-39657000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr18:39648200-39657200	Weak transcription	Lung	lung
33	chr18:39648200-39657200	Weak transcription	Osteobl	bone
34	chr18:39648200-39657600	Weak transcription	Brain Anterior Caudate	brain
35	chr18:39648200-39657800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr18:39648200-39662200	Weak transcription	Psoas Muscle	Psoas
37	chr18:39648200-39665400	Weak transcription	Spleen	Spleen
38	chr18:39648200-39666400	Weak transcription	Thymus	Thymus
39	chr18:39648200-39668200	Weak transcription	Brain Angular Gyrus	brain
40	chr18:39648400-39656400	Weak transcription	Fetal Brain Female	brain
41	chr18:39648400-39657000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr18:39648400-39657000	Weak transcription	Brain Germinal Matrix	brain
43	chr18:39648400-39657800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr18:39648400-39662200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr18:39648600-39658200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr18:39648800-39657200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr18:39649200-39665600	Weak transcription	HepG2	liver
48	chr18:39649200-39674600	Weak transcription	Fetal Intestine Small	intestine
49	chr18:39649600-39664400	Strong transcription	HSMM	muscle
50	chr18:39650000-39656400	Weak transcription	Fetal Muscle Leg	muscle

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