Variant report

Variant	rs3828481
Chromosome Location	chr4:56376664-56376665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10002541	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10005989	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10009593	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10016506	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026692	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10034433	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10462035	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133379	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133382	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11133383	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133394	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11133399	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726609	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733864	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11735267	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11931061	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11939815	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947476	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947623	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12646078	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12647034	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13102385	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13121235	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13128582	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13152650	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1522106	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1522107	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522108	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522110	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522111	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17085889	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873092	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1965467	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980273	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2130036	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2140077	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177129	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412646	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412647	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412663	0.82[EUR][1000 genomes]
rs28445925	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28448438	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28463765	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28469692	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28514423	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28525309	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28572116	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28582059	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28670674	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28673496	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28790098	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35767091	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736544	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736545	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3805147	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805152	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3805154	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805157	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817444	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371676	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4580704	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473005	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs480479	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4864998	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4865008	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs564762	0.84[EUR][1000 genomes]
rs576779	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59804446	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60797008	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60992571	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62303714	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62309727	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6554280	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6554286	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6554292	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6810948	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6811520	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6812042	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815516	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817267	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6817663	0.81[EUR][1000 genomes]
rs6819660	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824057	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824955	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825994	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6829182	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6832769	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6834676	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6837710	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6839788	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6846427	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850524	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6851838	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6853192	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726967	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667849	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7668147	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7670225	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7673908	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7677526	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7684810	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9312662	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9684708	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997288	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9998038	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998146	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56314400-56377200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr4:56332600-56377800	Weak transcription	Gastric	stomach
3	chr4:56336000-56376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:56337400-56377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:56341400-56385600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:56341600-56377000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:56341800-56376800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:56342200-56377600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:56342400-56378200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:56342800-56391400	Weak transcription	Psoas Muscle	Psoas
11	chr4:56344600-56378200	Weak transcription	Brain Germinal Matrix	brain
12	chr4:56355400-56377000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:56355400-56377000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:56355400-56377200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:56355400-56377400	Weak transcription	Brain Anterior Caudate	brain
16	chr4:56355400-56378000	Weak transcription	Aorta	Aorta
17	chr4:56355400-56379200	Weak transcription	Ovary	ovary
18	chr4:56355400-56379200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:56355400-56380800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:56355400-56381800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:56355400-56386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:56355600-56377000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr4:56355600-56377000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:56356800-56376800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:56361200-56387400	Weak transcription	Left Ventricle	heart
26	chr4:56361400-56377000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:56361400-56381000	Weak transcription	Fetal Brain Male	brain
28	chr4:56361600-56377200	Weak transcription	Adipose Nuclei	Adipose
29	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:56361800-56384400	Weak transcription	Primary B cells from cord blood	blood
31	chr4:56362000-56377200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:56364600-56376800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:56366200-56377000	Weak transcription	Spleen	Spleen
34	chr4:56366200-56377200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:56366200-56377200	Weak transcription	Lung	lung
36	chr4:56366200-56377600	Weak transcription	Liver	Liver
37	chr4:56366200-56386400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:56366800-56377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:56368600-56377000	Weak transcription	Right Ventricle	heart
40	chr4:56369600-56376800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:56369600-56377000	Weak transcription	Fetal Lung	lung
42	chr4:56370000-56377000	Weak transcription	HUVEC	blood vessel
43	chr4:56370000-56379200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:56370000-56379600	Weak transcription	NHDF-Ad	bronchial
45	chr4:56370000-56391200	Weak transcription	HSMM	muscle
46	chr4:56370200-56390800	Weak transcription	HMEC	breast
47	chr4:56372600-56405200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:56373600-56377600	Weak transcription	Fetal Intestine Small	intestine
49	chr4:56373600-56386000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:56374400-56379400	Weak transcription	A549	lung

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