Variant report

Variant	rs28394221
Chromosome Location	chr4:7890278-7890279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10049998	0.94[ASN][1000 genomes]
rs11932843	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13115701	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131154	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13137140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140004	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13145572	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146302	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13147998	0.93[ASN][1000 genomes]
rs1320073	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13435273	0.94[ASN][1000 genomes]
rs17770147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770177	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067842	0.82[ASN][1000 genomes]
rs28432831	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28492032	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28539821	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546404	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547902	0.88[AFR][1000 genomes]
rs28605531	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613311	0.90[ASN][1000 genomes]
rs28626087	0.89[AMR][1000 genomes]
rs28631977	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28644432	0.81[ASN][1000 genomes]
rs28655476	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28673208	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28688265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733584	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs28754920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891927	0.94[ASN][1000 genomes]
rs34072304	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34075381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34092549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34119140	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34121576	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34132874	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34181918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34189407	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34221000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34383852	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34392913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34570748	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34598003	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34652148	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34868842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869495	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34909423	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34982807	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35114566	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35138920	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35238070	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35349192	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35727635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35735994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881667	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35905776	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35933973	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35967175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36013696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36046241	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36106793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934540	0.85[ASN][1000 genomes]
rs4234831	0.85[ASN][1000 genomes]
rs4256209	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296663	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4361385	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4411970	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4443285	0.85[ASN][1000 genomes]
rs4447865	0.85[ASN][1000 genomes]
rs4487321	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4579115	0.81[ASN][1000 genomes]
rs4689875	0.85[ASN][1000 genomes]
rs4696742	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4696747	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4696762	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4696772	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62289341	0.97[ASN][1000 genomes]
rs62289351	0.97[ASN][1000 genomes]
rs6446624	0.85[ASN][1000 genomes]
rs6446625	0.85[ASN][1000 genomes]
rs6446627	0.88[ASN][1000 genomes]
rs6446629	0.88[ASN][1000 genomes]
rs6824266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826598	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6828574	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6829505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832352	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833054	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6837845	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838055	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855982	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71600561	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71601887	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601890	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660568	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682202	0.85[ASN][1000 genomes]
rs7682611	0.88[ASN][1000 genomes]
rs7691386	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694106	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7697255	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
6	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:7879400-7891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:7881800-7896600	Weak transcription	Lung	lung
9	chr4:7883000-7891800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:7883200-7891800	Weak transcription	Ovary	ovary
11	chr4:7883200-7893000	Weak transcription	Left Ventricle	heart
12	chr4:7883200-7904400	Weak transcription	Gastric	stomach
13	chr4:7884800-7892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
15	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
16	chr4:7887000-7890400	Enhancers	HSMMtube	muscle
17	chr4:7887200-7890600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:7887200-7891800	Weak transcription	HepG2	liver
19	chr4:7888200-7893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:7888600-7891800	Weak transcription	Brain Anterior Caudate	brain
21	chr4:7888800-7892000	Weak transcription	Brain Germinal Matrix	brain
22	chr4:7888800-7892400	Weak transcription	Fetal Brain Male	brain
23	chr4:7889000-7890400	Enhancers	Osteobl	bone
24	chr4:7889000-7891800	Weak transcription	Stomach Mucosa	stomach
25	chr4:7889000-7892400	Weak transcription	Adipose Nuclei	Adipose
26	chr4:7889000-7892600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:7889000-7892600	Weak transcription	Aorta	Aorta
28	chr4:7889200-7890400	Weak transcription	NHDF-Ad	bronchial
29	chr4:7889200-7892000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:7889200-7892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:7889400-7891800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:7889400-7891800	Weak transcription	HUVEC	blood vessel
34	chr4:7889400-7891800	Weak transcription	NHLF	lung
35	chr4:7889400-7892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:7889600-7890800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:7889600-7891400	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr4:7889600-7891800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:7889600-7892600	Weak transcription	Fetal Kidney	kidney
40	chr4:7889800-7890400	Enhancers	Colon Smooth Muscle	Colon
41	chr4:7889800-7890600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:7889800-7891600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:7889800-7891800	Weak transcription	Fetal Heart	heart
44	chr4:7889800-7891800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:7890000-7890400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:7890000-7890600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr4:7890000-7890600	ZNF genes & repeats	NHEK	skin
48	chr4:7890200-7891000	Weak transcription	Fetal Lung	lung
49	chr4:7890200-7891400	Weak transcription	NH-A	brain
50	chr4:7890200-7892200	Weak transcription	HSMM	muscle

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