Variant report

Variant	rs28845843
Chromosome Location	chr4:107009152-107009153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10000428	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003024	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004611	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008428	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10008773	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10016884	0.99[ASN][1000 genomes]
rs10017969	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10018910	1.00[ASN][1000 genomes]
rs10025052	0.83[EUR][1000 genomes]
rs10027207	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030019	0.83[EUR][1000 genomes]
rs10049933	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097912	0.83[EUR][1000 genomes]
rs11732251	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732791	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11932523	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942153	0.84[EUR][1000 genomes]
rs12509366	0.82[EUR][1000 genomes]
rs12509640	0.83[EUR][1000 genomes]
rs12510966	0.84[EUR][1000 genomes]
rs12512683	0.83[EUR][1000 genomes]
rs12513345	0.88[ASN][1000 genomes]
rs12642691	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642900	0.81[EUR][1000 genomes]
rs12650692	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	1.00[ASN][1000 genomes]
rs28391259	0.83[EUR][1000 genomes]
rs28394440	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28467469	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28784652	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28805707	0.99[ASN][1000 genomes]
rs28822186	0.83[EUR][1000 genomes]
rs28897193	0.83[EUR][1000 genomes]
rs3109958	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109960	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113250	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4306956	0.93[EUR][1000 genomes]
rs4307042	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4314353	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355394	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4364267	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4374692	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4470632	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4508971	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569824	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577583	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600995	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55633564	0.84[EUR][1000 genomes]
rs60538413	0.95[EUR][1000 genomes]
rs62321365	0.83[EUR][1000 genomes]
rs6533237	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823347	0.83[EUR][1000 genomes]
rs6824682	0.84[EUR][1000 genomes]
rs6828362	0.82[EUR][1000 genomes]
rs6836198	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6842919	0.95[EUR][1000 genomes]
rs6843331	0.96[EUR][1000 genomes]
rs6844105	1.00[ASN][1000 genomes]
rs6846579	0.83[EUR][1000 genomes]
rs6849573	1.00[ASN][1000 genomes]
rs6852388	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853554	0.88[ASN][1000 genomes]
rs72677306	0.83[EUR][1000 genomes]
rs7356287	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7438546	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657962	0.84[EUR][1000 genomes]
rs7662592	0.83[EUR][1000 genomes]
rs7667596	0.95[ASN][1000 genomes]
rs7668276	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677248	0.83[EUR][1000 genomes]
rs7678847	0.83[EUR][1000 genomes]
rs7682646	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687657	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7689298	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692069	0.84[EUR][1000 genomes]
rs7692652	0.91[ASN][1000 genomes]
rs7693333	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693448	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685464	0.82[EUR][1000 genomes]
rs9991091	0.83[EUR][1000 genomes]
rs9996093	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[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	esv3414280	chr4:106987397-107017178	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv3419151	chr4:106987397-107020894	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28845843	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs28845843	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106984000-107010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:106985000-107011400	Weak transcription	HepG2	liver
3	chr4:106993200-107010000	Weak transcription	Left Ventricle	heart
4	chr4:106993400-107010400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:106993600-107010000	Weak transcription	Right Ventricle	heart
6	chr4:106993800-107010800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:106994600-107015000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:106994800-107011600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:106995200-107010000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:106995200-107011400	Weak transcription	Colonic Mucosa	Colon
11	chr4:106995400-107011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:106995400-107011000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:106995600-107010400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:106996000-107010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:106997200-107031000	Weak transcription	Psoas Muscle	Psoas
16	chr4:106998000-107010000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:106998600-107010200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:106998600-107010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:106998600-107010800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:106999000-107011000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:106999000-107011800	Weak transcription	Fetal Heart	heart
22	chr4:106999000-107012000	Weak transcription	NHDF-Ad	bronchial
23	chr4:106999200-107010000	Weak transcription	Fetal Brain Male	brain
24	chr4:106999200-107010400	Weak transcription	HSMM	muscle
25	chr4:107000000-107011400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:107000200-107010000	Weak transcription	Brain Angular Gyrus	brain
27	chr4:107001000-107010200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:107001200-107018600	Weak transcription	HUVEC	blood vessel
29	chr4:107001600-107010200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:107001600-107010200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:107002800-107009600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:107002800-107010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:107002800-107010000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:107002800-107010000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:107002800-107011400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:107003000-107010000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:107003000-107010400	Weak transcription	Brain Substantia Nigra	brain
38	chr4:107003200-107010200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:107003600-107010800	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:107003800-107010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:107004200-107009800	Weak transcription	Liver	Liver
42	chr4:107004200-107010000	Weak transcription	Pancreas	Pancrea
43	chr4:107004200-107011000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:107004600-107009800	Weak transcription	Lung	lung
45	chr4:107004600-107010400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:107004600-107010800	Weak transcription	Gastric	stomach
47	chr4:107004600-107011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:107004800-107010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:107004800-107010000	Weak transcription	Esophagus	oesophagus
50	chr4:107005000-107010000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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