Variant report

Variant	rs28831670
Chromosome Location	chr4:121728827-121728828
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10006287	0.83[AFR][1000 genomes]
rs10026047	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10033707	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11098589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1349347	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376099	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397770	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450462	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168226	0.86[AFR][1000 genomes]
rs17051263	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868715	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1877214	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1877215	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1912720	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987468	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2100237	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136997	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237212	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2597536	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597537	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597538	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2597540	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667172	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667173	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28810489	0.86[AFR][1000 genomes]
rs28850273	0.84[EUR][1000 genomes]
rs343181	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343184	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343187	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343190	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343192	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3789141	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789142	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804174	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4833183	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4833184	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4833675	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4833676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833681	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57841364	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59085467	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59837089	0.83[EUR][1000 genomes]
rs6835471	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	nsv879855	chr4:121691899-121747335	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv879856	chr4:121697932-121737767	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv879857	chr4:121697932-121747335	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv879858	chr4:121703336-121747335	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121673000-121737400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:121695800-121730000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:121707200-121730600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:121710200-121729600	Weak transcription	Esophagus	oesophagus
5	chr4:121715400-121729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:121718600-121730800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:121720600-121731400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:121722800-121729000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:121722800-121729800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:121722800-121730400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:121722800-121733000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:121722800-121737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:121723000-121729600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:121723000-121729800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:121723000-121730000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:121723000-121730600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:121723000-121730600	Weak transcription	NHDF-Ad	bronchial
18	chr4:121723000-121738000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:121723600-121743000	Weak transcription	Fetal Heart	heart
20	chr4:121723800-121729600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:121726400-121743400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:121727200-121739000	Weak transcription	Gastric	stomach
23	chr4:121727600-121729600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:121728200-121729000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr4:121728200-121732000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr4:121728400-121729000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:121728400-121729000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:121728400-121729000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr4:121728400-121729200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:121728400-121729600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr4:121728400-121730000	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:121728600-121729000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:121728600-121729000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:121728600-121729200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:121728600-121729400	Strong transcription	Left Ventricle	heart
36	chr4:121728600-121729800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:121728600-121730200	Strong transcription	Ovary	ovary
38	chr4:121728600-121730400	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr4:121728600-121732200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:121728800-121729000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr4:121728800-121729200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr4:121728800-121729200	Strong transcription	Fetal Stomach	stomach
43	chr4:121728800-121730000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:121728800-121730200	Strong transcription	Fetal Muscle Leg	muscle
45	chr4:121728800-121730400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:121728800-121730400	ZNF genes & repeats	Aorta	Aorta
47	chr4:121728800-121730400	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr4:121728800-121730400	ZNF genes & repeats	Lung	lung
49	chr4:121728800-121730400	Strong transcription	Pancreas	Pancrea
50	chr4:121728800-121732000	Strong transcription	Fetal Lung	lung

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