Variant report

Variant	rs3732896
Chromosome Location	chr3:100712059-100712060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10936459	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936460	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs13062274	0.87[ASN][1000 genomes]
rs13066740	0.99[ASN][1000 genomes]
rs13072542	0.87[ASN][1000 genomes]
rs13075849	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079773	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13080505	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082728	0.87[ASN][1000 genomes]
rs13090397	0.87[ASN][1000 genomes]
rs13091963	0.98[ASN][1000 genomes]
rs1349198	0.83[CHB][hapmap];0.81[AFR][1000 genomes]
rs1449300	0.87[ASN][1000 genomes]
rs1449302	0.87[ASN][1000 genomes]
rs1449305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449306	0.84[CHB][hapmap];0.81[AFR][1000 genomes]
rs1449308	0.85[CHB][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.86[YRI][hapmap]
rs1449309	0.81[YRI][hapmap]
rs1449315	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449320	0.87[ASN][1000 genomes]
rs16843113	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843148	0.87[ASN][1000 genomes]
rs16843163	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254374	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595914	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595917	0.99[ASN][1000 genomes]
rs2713757	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2713768	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713769	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713771	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713773	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2713774	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713775	0.99[ASN][1000 genomes]
rs2713776	0.99[ASN][1000 genomes]
rs28365990	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873448	0.87[ASN][1000 genomes]
rs34350012	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34587221	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34670326	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748077	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35064087	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35290466	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732895	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806655	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273569	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928060	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928102	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs4928104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56847573	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58004340	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7631509	0.87[ASN][1000 genomes]
rs9849371	0.83[YRI][hapmap]
rs9853097	0.84[CHB][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3732896	C3orf26	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100709000-100712600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:100709200-100713000	Active TSS	Stomach Smooth Muscle	stomach
3	chr3:100709600-100712400	Active TSS	HSMMtube	muscle
4	chr3:100709800-100712400	Active TSS	Fetal Muscle Leg	muscle
5	chr3:100709800-100712400	Active TSS	NHDF-Ad	bronchial
6	chr3:100709800-100712600	Active TSS	Muscle Satellite Cultured Cells	--
7	chr3:100709800-100712600	Active TSS	Fetal Stomach	stomach
8	chr3:100710000-100712800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:100710000-100712800	Active TSS	Fetal Lung	lung
10	chr3:100710200-100712200	Active TSS	Right Atrium	heart
11	chr3:100710200-100712400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr3:100710200-100712600	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:100710400-100712400	Active TSS	Colon Smooth Muscle	Colon
14	chr3:100710400-100712400	Active TSS	NHLF	lung
15	chr3:100710400-100712800	Active TSS	Rectal Smooth Muscle	rectum
16	chr3:100710600-100712400	Active TSS	Ovary	ovary
17	chr3:100710600-100712400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr3:100710600-100712600	Active TSS	Fetal Intestine Large	intestine
19	chr3:100710800-100712200	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:100710800-100712400	Active TSS	Fetal Intestine Small	intestine
21	chr3:100710800-100712400	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:100711000-100712200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:100711000-100712200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:100711000-100712200	Active TSS	Left Ventricle	heart
25	chr3:100711000-100712400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:100711000-100712400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:100711000-100712400	Active TSS	Aorta	Aorta
28	chr3:100711000-100712400	Active TSS	Brain Anterior Caudate	brain
29	chr3:100711000-100712400	Active TSS	Brain Substantia Nigra	brain
30	chr3:100711000-100712400	Active TSS	Colonic Mucosa	Colon
31	chr3:100711000-100712400	Active TSS	Psoas Muscle	Psoas
32	chr3:100711000-100712400	Flanking Active TSS	NHEK	skin
33	chr3:100711200-100712200	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:100711200-100712200	Active TSS	Esophagus	oesophagus
35	chr3:100711200-100712200	Active TSS	Placenta	Placenta
36	chr3:100711200-100712200	Active TSS	Right Ventricle	heart
37	chr3:100711200-100712400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:100711200-100712600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:100711200-100712800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:100711400-100712400	Flanking Active TSS	HUVEC	blood vessel
41	chr3:100711600-100712200	Active TSS	Liver	Liver
42	chr3:100711600-100712400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:100711600-100712400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr3:100711600-100712400	Enhancers	HMEC	breast
45	chr3:100711600-100712400	Flanking Active TSS	HSMM	muscle
46	chr3:100711600-100712800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:100711800-100712200	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:100711800-100712400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:100711800-100712400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:100711800-100712400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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