Variant report

Variant	rs56222430
Chromosome Location	chr4:106994648-106994649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 192 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:190)

rs_ID	r²[population]
rs10002288	0.90[ASN][1000 genomes]
rs10025052	0.90[ASN][1000 genomes]
rs10030019	0.91[ASN][1000 genomes]
rs10084928	0.91[ASN][1000 genomes]
rs10516532	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516533	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097912	0.91[ASN][1000 genomes]
rs11097914	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097916	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097917	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097919	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097924	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097925	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11942153	0.90[ASN][1000 genomes]
rs12499891	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12500775	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12502764	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12503753	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12504704	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504721	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12505689	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12506062	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506658	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12507429	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507867	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12507874	0.83[ASN][1000 genomes]
rs12508432	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12508552	0.91[ASN][1000 genomes]
rs12509366	0.91[ASN][1000 genomes]
rs12509640	1.00[ASN][1000 genomes]
rs12509865	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12510058	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12510966	0.91[ASN][1000 genomes]
rs12511305	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512683	0.91[ASN][1000 genomes]
rs12512877	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12512903	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12512966	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12513317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639678	0.87[ASN][1000 genomes]
rs12639869	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641015	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641037	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12642059	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12642227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12642900	0.91[ASN][1000 genomes]
rs12643397	0.91[ASN][1000 genomes]
rs12644259	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12644596	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12645255	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645271	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645698	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12645743	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12646263	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12646485	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12647078	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649709	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12651360	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17036613	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17259572	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17273093	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17273445	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17274017	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17274248	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333287	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333732	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333879	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17333899	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1988695	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2290607	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28391259	0.91[ASN][1000 genomes]
rs28507027	0.91[ASN][1000 genomes]
rs28765420	0.89[ASN][1000 genomes]
rs28787305	0.91[ASN][1000 genomes]
rs28814088	0.87[ASN][1000 genomes]
rs28822186	0.91[ASN][1000 genomes]
rs28866820	0.91[ASN][1000 genomes]
rs28868894	0.91[ASN][1000 genomes]
rs28875879	0.91[ASN][1000 genomes]
rs28897193	0.91[ASN][1000 genomes]
rs34193646	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34899289	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34961213	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35518913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775090	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4323181	0.91[ASN][1000 genomes]
rs4337798	0.91[ASN][1000 genomes]
rs4337799	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339284	0.91[ASN][1000 genomes]
rs4422480	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4429790	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4458525	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4466113	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4481295	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4521418	0.90[ASN][1000 genomes]
rs4607300	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4645291	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55633564	0.91[ASN][1000 genomes]
rs55634475	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55710349	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55833794	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56009469	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56135499	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56231393	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56260521	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56329826	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56333662	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56341229	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56775039	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56833325	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57246774	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59784613	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60538413	0.80[ASN][1000 genomes]
rs61256759	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61544154	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62321365	0.89[ASN][1000 genomes]
rs6533240	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533243	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533245	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533246	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6810877	0.89[ASN][1000 genomes]
rs6815014	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816614	0.91[ASN][1000 genomes]
rs6816698	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6818197	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6818626	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822692	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6823347	0.90[ASN][1000 genomes]
rs6824682	0.91[ASN][1000 genomes]
rs6827816	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6828362	0.91[ASN][1000 genomes]
rs6829795	0.91[ASN][1000 genomes]
rs6831665	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6835216	0.91[ASN][1000 genomes]
rs6838283	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6842919	0.89[ASN][1000 genomes]
rs6843331	0.89[ASN][1000 genomes]
rs6843870	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844324	0.91[ASN][1000 genomes]
rs6846579	0.91[ASN][1000 genomes]
rs72489522	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72677306	0.91[ASN][1000 genomes]
rs72876575	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72876590	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72876592	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72876594	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72878537	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72893620	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7340989	0.84[ASN][1000 genomes]
rs73839422	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7655054	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657962	0.89[ASN][1000 genomes]
rs7657975	0.91[ASN][1000 genomes]
rs7658011	0.90[ASN][1000 genomes]
rs7658701	0.91[ASN][1000 genomes]
rs7661499	0.83[ASN][1000 genomes]
rs7661565	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7662219	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7662291	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7662395	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7662592	0.91[ASN][1000 genomes]
rs7662806	0.91[ASN][1000 genomes]
rs7662836	0.91[ASN][1000 genomes]
rs7664032	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664188	0.91[ASN][1000 genomes]
rs7665946	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7667719	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7668477	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7669087	0.91[ASN][1000 genomes]
rs7669212	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671145	0.89[ASN][1000 genomes]
rs7673949	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7674381	0.83[ASN][1000 genomes]
rs7674466	0.87[ASN][1000 genomes]
rs7674931	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7675728	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7677248	0.90[ASN][1000 genomes]
rs7678229	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7678847	0.90[ASN][1000 genomes]
rs7681257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7688008	0.85[EUR][1000 genomes]
rs7688411	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7692069	0.86[ASN][1000 genomes]
rs7697996	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7698386	0.92[ASN][1000 genomes]
rs7699768	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9684658	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9685018	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9685464	0.91[ASN][1000 genomes]
rs9991091	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56222430	MGC16169	cis	multi-tissue	Pritchard
rs56222430	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs56222430	MGC16169	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106972400-106997000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:106983800-106994800	Weak transcription	Fetal Kidney	kidney
3	chr4:106983800-106995000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:106984000-106995000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:106984000-107010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:106984600-106998200	Weak transcription	Fetal Heart	heart
7	chr4:106985000-107011400	Weak transcription	HepG2	liver
8	chr4:106986800-107002400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:106987000-106995800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:106988000-106994800	Weak transcription	Aorta	Aorta
11	chr4:106990000-106998000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:106992400-106998000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:106992600-106994800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:106993000-107008800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:106993200-106997000	Weak transcription	Gastric	stomach
16	chr4:106993200-106997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:106993200-106997800	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:106993200-107010000	Weak transcription	Left Ventricle	heart
19	chr4:106993400-106998200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:106993400-107010400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:106993600-106998200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:106993600-106998400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:106993600-107002400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:106993600-107010000	Weak transcription	Right Ventricle	heart
25	chr4:106993800-106995000	Weak transcription	Pancreas	Pancrea
26	chr4:106993800-107010800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:106994000-106994800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:106994200-106994800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:106994200-106994800	Weak transcription	Ovary	ovary
30	chr4:106994400-106994800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:106994400-106994800	Weak transcription	Primary T cells from cord blood	blood
32	chr4:106994400-106996200	ZNF genes & repeats	Liver	Liver
33	chr4:106994400-106997000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr4:106994400-106997000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:106994400-106998400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:106994600-106994800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:106994600-106995200	ZNF genes & repeats	Fetal Lung	lung
38	chr4:106994600-106995200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
39	chr4:106994600-106995400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
40	chr4:106994600-106995400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:106994600-106995400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:106994600-106995400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr4:106994600-106995400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr4:106994600-106995400	ZNF genes & repeats	Fetal Stomach	stomach
45	chr4:106994600-106996200	ZNF genes & repeats	Fetal Intestine Large	intestine
46	chr4:106994600-106996200	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr4:106994600-106996200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr4:106994600-106997000	Weak transcription	HSMM	muscle
49	chr4:106994600-106998400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:106994600-107015000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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