Variant report

Variant	rs3828340
Chromosome Location	chr2:48807976-48807977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10495953	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125176	0.86[EUR][1000 genomes]
rs11676150	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11678306	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680574	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681276	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11681426	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683611	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11693429	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11693559	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693691	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475789	0.98[ASN][1000 genomes]
rs12990079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12992870	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12999304	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13010692	0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011288	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13014112	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13016899	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13025488	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13027618	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030948	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031184	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13034063	0.84[EUR][1000 genomes]
rs13034951	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037412	0.95[CHB][hapmap]
rs17039250	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996970	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2103112	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177489	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293270	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293271	0.81[ASN][1000 genomes]
rs2293272	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2349098	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2882084	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749142	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3749144	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749145	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792234	0.88[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3792235	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792236	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792237	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792238	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4566410	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4953593	0.85[EUR][1000 genomes]
rs55641971	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700200	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55858189	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56111874	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62135201	0.82[EUR][1000 genomes]
rs62135230	0.93[ASN][1000 genomes]
rs62135231	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135232	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62135233	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62135236	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545048	0.90[ASN][1000 genomes]
rs66888174	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6709043	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710565	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6712592	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6712724	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716291	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[ASN][1000 genomes]
rs6722556	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727929	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6729860	0.80[EUR][1000 genomes]
rs6732365	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6737732	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6741341	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6741677	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742725	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757847	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761796	0.99[ASN][1000 genomes]
rs940389	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3828340	FOXN2	cis	parietal	SCAN
rs3828340	STON1	cis	Esophagus Muscularis	GTEx
rs3828340	STON1-GTF2A1L	cis	cerebellum	SCAN
rs3828340	STON1-GTF2A1L	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:48773000-48808800	Weak transcription	Right Ventricle	heart
3	chr2:48788600-48812000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:48794400-48812000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:48794400-48827200	Weak transcription	NHDF-Ad	bronchial
6	chr2:48794600-48811200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:48795400-48812000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:48795400-48814200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:48795600-48808000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:48795600-48826000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:48798800-48808000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:48798800-48815600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:48799000-48825800	Weak transcription	HSMMtube	muscle
14	chr2:48800000-48812000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:48800400-48808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:48800400-48808000	Weak transcription	Fetal Kidney	kidney
17	chr2:48800400-48811800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:48800400-48812600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:48800400-48813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:48800400-48814000	Weak transcription	Lung	lung
21	chr2:48800600-48811600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:48800600-48811800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:48800800-48812800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:48801600-48810200	Weak transcription	Placenta	Placenta
25	chr2:48803400-48812000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:48804600-48824600	Weak transcription	Fetal Intestine Large	intestine
27	chr2:48804800-48816200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:48806600-48811800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:48807600-48813600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:48807800-48808200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:48807800-48808200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:48807800-48808400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:48807800-48808400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:48807800-48808600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:48807800-48808600	Strong transcription	Psoas Muscle	Psoas
36	chr2:48807800-48808800	Strong transcription	Adipose Nuclei	Adipose
37	chr2:48807800-48809000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:48807800-48809000	Genic enhancers	Colon Smooth Muscle	Colon
39	chr2:48807800-48809000	Strong transcription	Left Ventricle	heart
40	chr2:48807800-48809600	Strong transcription	Aorta	Aorta
41	chr2:48807800-48809600	Strong transcription	Fetal Lung	lung
42	chr2:48807800-48809600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:48807800-48809600	Strong transcription	Ovary	ovary
44	chr2:48807800-48809800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:48807800-48810200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:48807800-48810600	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:48807800-48812800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr2:48807800-48814200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:48807800-48815200	Strong transcription	Fetal Stomach	stomach
50	chr2:48807800-48815400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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