Variant report

Variant	rs28467469
Chromosome Location	chr4:107036627-107036628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10000428	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003024	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004611	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008428	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008773	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10016884	0.99[ASN][1000 genomes]
rs10017969	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10018910	1.00[ASN][1000 genomes]
rs10025052	0.81[EUR][1000 genomes]
rs10027207	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030019	0.80[EUR][1000 genomes]
rs10049933	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097912	0.80[EUR][1000 genomes]
rs11732251	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732791	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942153	0.81[EUR][1000 genomes]
rs12510966	0.81[EUR][1000 genomes]
rs12512683	0.80[EUR][1000 genomes]
rs12513345	0.88[ASN][1000 genomes]
rs12642691	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	1.00[ASN][1000 genomes]
rs2691804	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28391259	0.81[EUR][1000 genomes]
rs28394440	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28784652	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28805707	0.99[ASN][1000 genomes]
rs28845843	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28897193	0.82[EUR][1000 genomes]
rs2949625	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109953	0.94[ASN][1000 genomes]
rs3109955	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109958	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109960	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113250	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3133168	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4306956	0.90[EUR][1000 genomes]
rs4307042	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4314353	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355394	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4364267	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4374692	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470632	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4508971	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569824	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577583	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600995	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55633564	0.81[EUR][1000 genomes]
rs60538413	0.92[EUR][1000 genomes]
rs62321365	0.81[EUR][1000 genomes]
rs6533237	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533242	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823347	0.82[EUR][1000 genomes]
rs6824682	0.80[EUR][1000 genomes]
rs6828362	0.80[EUR][1000 genomes]
rs6836198	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842919	0.91[EUR][1000 genomes]
rs6843331	0.92[EUR][1000 genomes]
rs6844105	1.00[ASN][1000 genomes]
rs6846579	0.82[EUR][1000 genomes]
rs6849573	1.00[ASN][1000 genomes]
rs6852388	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853554	0.88[ASN][1000 genomes]
rs7356287	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7438546	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657962	0.81[EUR][1000 genomes]
rs7667596	0.95[ASN][1000 genomes]
rs7668276	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677248	0.81[EUR][1000 genomes]
rs7682646	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687657	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7689298	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692069	0.81[EUR][1000 genomes]
rs7692652	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7693333	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693448	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685464	0.80[EUR][1000 genomes]
rs9996093	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv511247	chr4:107022702-107065220	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv879701	chr4:107024776-107163128	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28467469	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs28467469	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107012600-107038400	Weak transcription	NHDF-Ad	bronchial
2	chr4:107029000-107037800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:107029800-107038000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:107030800-107037800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:107031600-107052600	Weak transcription	Fetal Thymus	thymus
6	chr4:107031800-107039400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:107031800-107053400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:107032000-107052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:107032000-107058200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:107032200-107038400	Weak transcription	Fetal Brain Male	brain
11	chr4:107032400-107037000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:107032600-107039600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:107033400-107039800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:107033400-107053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:107033600-107037600	Strong transcription	Brain Hippocampus Middle	brain
16	chr4:107033600-107037800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:107033600-107038000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:107033600-107052800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:107033600-107053400	Weak transcription	Osteobl	bone
20	chr4:107033800-107036800	Weak transcription	Brain Substantia Nigra	brain
21	chr4:107033800-107037800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:107033800-107038200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:107033800-107038400	Strong transcription	Primary T cells from cord blood	blood
24	chr4:107033800-107039000	Weak transcription	HSMMtube	muscle
25	chr4:107033800-107053400	Weak transcription	HSMM	muscle
26	chr4:107034000-107037800	Strong transcription	Adipose Nuclei	Adipose
27	chr4:107034000-107038000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr4:107034000-107038400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:107034200-107036800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:107034200-107036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr4:107034200-107036800	Weak transcription	Fetal Kidney	kidney
32	chr4:107034200-107037400	Strong transcription	Placenta	Placenta
33	chr4:107034200-107037600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:107034200-107037800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:107034200-107038600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:107034200-107040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:107034200-107053400	Weak transcription	Right Ventricle	heart
38	chr4:107034400-107037600	Strong transcription	GM12878-XiMat	blood
39	chr4:107034400-107038000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:107034600-107037000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:107034600-107038000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:107034800-107037200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:107034800-107037600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:107034800-107037600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:107034800-107038000	Strong transcription	Primary B cells from cord blood	blood
46	chr4:107034800-107038000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:107034800-107038000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:107034800-107038400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:107034800-107041000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:107035000-107037600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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