Variant report

Variant	rs28464398
Chromosome Location	chr4:99342964-99342965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10001137	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027340	0.87[EUR][1000 genomes]
rs17027393	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	0.83[AMR][1000 genomes]
rs28494643	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28503871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28731135	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55993060	0.87[EUR][1000 genomes]
rs56805018	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.83[AMR][1000 genomes]
rs60281573	0.87[EUR][1000 genomes]
rs60544326	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60638903	0.87[EUR][1000 genomes]
rs6831386	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.83[AMR][1000 genomes]
rs73832145	0.87[EUR][1000 genomes]
rs73832149	0.87[EUR][1000 genomes]
rs73832156	0.87[EUR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7656868	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.91[AMR][1000 genomes];1.00[EUR][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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99290600-99346000	Weak transcription	Fetal Lung	lung
2	chr4:99299400-99350800	Weak transcription	NHLF	lung
3	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
4	chr4:99308600-99363200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:99312000-99355400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:99325800-99367000	Weak transcription	Right Ventricle	heart
7	chr4:99327800-99355400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:99334000-99355000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:99334200-99345000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:99334200-99350800	Weak transcription	NHEK	skin
11	chr4:99334200-99355200	Weak transcription	Fetal Kidney	kidney
12	chr4:99334200-99355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:99334400-99343000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:99334400-99343800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:99334400-99344800	Weak transcription	Fetal Intestine Small	intestine
16	chr4:99334400-99345200	Weak transcription	Brain Germinal Matrix	brain
17	chr4:99334400-99355200	Weak transcription	Fetal Intestine Large	intestine
18	chr4:99334400-99361800	Weak transcription	Aorta	Aorta
19	chr4:99334400-99364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:99334400-99366000	Weak transcription	Psoas Muscle	Psoas
21	chr4:99334400-99367400	Weak transcription	Small Intestine	intestine
22	chr4:99334400-99368800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:99336400-99365000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:99337200-99356000	Weak transcription	Esophagus	oesophagus
25	chr4:99337200-99363200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:99337600-99351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:99337600-99369800	Weak transcription	Fetal Heart	heart
28	chr4:99337800-99343800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:99337800-99346200	Strong transcription	Primary B cells from cord blood	blood
30	chr4:99337800-99346400	Strong transcription	Dnd41	blood
31	chr4:99337800-99346600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr4:99337800-99346600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:99337800-99346800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr4:99337800-99346800	Strong transcription	Adipose Nuclei	Adipose
35	chr4:99337800-99347000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:99337800-99347400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:99338000-99344400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:99338000-99344600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:99338000-99344600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:99338000-99346200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:99338000-99346800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:99338000-99347000	Strong transcription	HSMM	muscle
43	chr4:99338000-99347400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:99338000-99347600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:99338200-99343200	Strong transcription	NHDF-Ad	bronchial
46	chr4:99338200-99343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:99338200-99346800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr4:99338400-99345600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:99338400-99363200	Weak transcription	Spleen	Spleen
50	chr4:99338600-99345200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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