Variant report

Variant	rs6105098
Chromosome Location	chr20:13417386-13417387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs13039162	0.91[ASN][1000 genomes]
rs13042843	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2070334	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073324	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2103972	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2182708	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2208207	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2208208	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273480	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747931	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789342	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3789347	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789348	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813131	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814236	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4814238	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4814242	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57218913	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042106	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6042128	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6042153	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074611	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6074612	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074613	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074618	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6074627	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6079066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079072	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079074	0.96[ASN][1000 genomes]
rs6079075	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079077	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079085	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079095	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079106	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6105096	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105103	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6105113	0.92[ASN][1000 genomes]
rs6109887	0.96[ASN][1000 genomes]
rs6109891	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6109903	0.88[ASN][1000 genomes]
rs6109905	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6109958	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6131483	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6131485	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131488	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6134879	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6134902	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134912	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73086013	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13379200-13463000	Weak transcription	HSMM	muscle
2	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
3	chr20:13395600-13477800	Weak transcription	Gastric	stomach
4	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr20:13398200-13417800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:13399800-13430800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:13403800-13435000	Weak transcription	HMEC	breast
8	chr20:13404400-13434800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:13404400-13434800	Weak transcription	NHEK	skin
10	chr20:13406800-13417400	Weak transcription	Colon Smooth Muscle	Colon
11	chr20:13408000-13417400	Weak transcription	Fetal Brain Female	brain
12	chr20:13408000-13419600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:13409000-13419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr20:13409200-13417400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr20:13410000-13421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr20:13410600-13417400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr20:13411400-13417400	Weak transcription	Fetal Stomach	stomach
18	chr20:13411400-13435000	Weak transcription	Lung	lung
19	chr20:13411600-13421400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr20:13412400-13417600	Strong transcription	Dnd41	blood
21	chr20:13412600-13421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:13412600-13424200	Weak transcription	HepG2	liver
23	chr20:13412800-13420600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr20:13413200-13417800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr20:13413600-13433400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:13414800-13417400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr20:13415000-13417400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:13415200-13417600	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr20:13415200-13428000	Weak transcription	Thymus	Thymus
30	chr20:13415400-13417400	Weak transcription	Fetal Intestine Large	intestine
31	chr20:13415400-13418000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr20:13415400-13419000	Weak transcription	Fetal Muscle Leg	muscle
33	chr20:13415400-13419400	Weak transcription	Fetal Lung	lung
34	chr20:13415400-13420400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr20:13415400-13420600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr20:13415400-13435000	Weak transcription	Placenta	Placenta
37	chr20:13415600-13417800	Weak transcription	Liver	Liver
38	chr20:13415600-13418600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr20:13415600-13433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr20:13415800-13417400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr20:13415800-13417400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr20:13415800-13417800	Weak transcription	Fetal Intestine Small	intestine
43	chr20:13415800-13419200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr20:13415800-13419600	Weak transcription	Ovary	ovary
45	chr20:13416000-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr20:13416000-13438200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr20:13416200-13417400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr20:13416200-13420800	Weak transcription	Primary B cells from cord blood	blood
49	chr20:13416200-13421000	Weak transcription	Primary T cells from cord blood	blood
50	chr20:13416200-13435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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