Variant report

Variant	rs3805546
Chromosome Location	chr5:146797394-146797395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11167988	0.84[AMR][1000 genomes]
rs12514302	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12515377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518292	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12653560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655492	1.00[AFR][1000 genomes]
rs12657809	0.81[CHB][hapmap];1.00[EUR][1000 genomes]
rs1432853	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432854	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432855	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432856	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432857	0.86[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106560	0.84[AMR][1000 genomes]
rs17106572	0.84[AMR][1000 genomes]
rs17106679	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106682	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106683	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106686	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106688	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106689	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106690	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17106698	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106709	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17106713	0.80[CHB][hapmap];1.00[EUR][1000 genomes]
rs17106716	0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17106723	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2288800	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288805	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2288809	0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2304043	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2304047	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3213857	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35439984	1.00[AFR][1000 genomes]
rs3792837	0.80[AMR][1000 genomes]
rs3792839	0.93[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792840	0.92[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792841	0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792843	0.93[ASN][1000 genomes]
rs3792844	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792845	0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792846	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805534	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs3805535	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs3805538	0.94[ASN][1000 genomes]
rs3805539	0.93[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805540	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805542	0.88[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805544	0.92[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816012	0.94[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6891468	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897123	0.80[CHB][hapmap];1.00[EUR][1000 genomes]
rs930213	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:146774000-146799400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:146777600-146800600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr5:146779800-146798400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:146783400-146800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:146784600-146800400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:146784800-146807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:146785400-146808800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:146787000-146798800	Weak transcription	Right Ventricle	heart
18	chr5:146789000-146798000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:146791200-146798200	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr5:146791600-146797800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr5:146792600-146798800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:146795000-146797800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:146795400-146797800	Enhancers	Ovary	ovary
24	chr5:146795400-146798200	Genic enhancers	NH-A	brain
25	chr5:146795600-146798000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:146795800-146797600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:146795800-146798200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr5:146795800-146800000	Enhancers	Rectal Smooth Muscle	rectum
29	chr5:146796000-146798200	Genic enhancers	Fetal Stomach	stomach
30	chr5:146796200-146798000	Enhancers	Fetal Intestine Large	intestine
31	chr5:146796400-146797800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:146796400-146797800	Enhancers	Fetal Lung	lung
33	chr5:146796400-146798000	Enhancers	Fetal Heart	heart
34	chr5:146796600-146797400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:146796600-146797400	Enhancers	Stomach Mucosa	stomach
36	chr5:146796600-146797400	Enhancers	NHDF-Ad	bronchial
37	chr5:146796600-146797600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:146796600-146797600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:146796600-146797600	Genic enhancers	Fetal Brain Female	brain
40	chr5:146796600-146797800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr5:146796600-146797800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr5:146796600-146797800	Enhancers	Psoas Muscle	Psoas
43	chr5:146796600-146798200	Enhancers	Fetal Intestine Small	intestine
44	chr5:146796600-146798200	Enhancers	NHLF	lung
45	chr5:146796800-146797400	Enhancers	Spleen	Spleen
46	chr5:146796800-146797600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:146796800-146797600	Enhancers	Aorta	Aorta
48	chr5:146796800-146797600	Genic enhancers	Fetal Brain Male	brain
49	chr5:146796800-146797800	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr5:146796800-146797800	Enhancers	Left Ventricle	heart

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