Variant report

Variant	rs3828378
Chromosome Location	chr3:145933485-145933486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10460850	0.92[ASN][1000 genomes]
rs10935609	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11926040	0.93[ASN][1000 genomes]
rs12488776	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629875	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13073184	0.96[CHB][hapmap];0.84[ASN][1000 genomes]
rs13079270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13086427	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1398527	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1512894	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175669	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867080	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34773907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35187466	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35499991	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35616919	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828379	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3920230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61207913	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808115	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836419	0.84[YRI][hapmap]

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	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	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	chr3:145897000-145933600	Weak transcription	Fetal Stomach	stomach
2	chr3:145903000-145934800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:145905000-145933600	Weak transcription	NHLF	lung
4	chr3:145907000-145938600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:145907600-145939200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:145908200-145936400	Weak transcription	A549	lung
7	chr3:145909600-145939200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:145910400-145940000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:145913800-145939200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:145914200-145937000	Weak transcription	Placenta	Placenta
11	chr3:145914600-145940200	Weak transcription	Gastric	stomach
12	chr3:145914800-145940200	Weak transcription	Psoas Muscle	Psoas
13	chr3:145914800-145940400	Weak transcription	Spleen	Spleen
14	chr3:145917800-145940400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:145918000-145940400	Weak transcription	Pancreas	Pancrea
16	chr3:145918400-145940400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:145919000-145934800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:145920600-145940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:145921600-145940200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:145922000-145934800	Weak transcription	Left Ventricle	heart
21	chr3:145922200-145935000	Weak transcription	NHDF-Ad	bronchial
22	chr3:145922600-145940400	Weak transcription	Lung	lung
23	chr3:145924400-145939200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
26	chr3:145924600-145934400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:145924600-145937200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:145924600-145939000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:145924600-145940200	Weak transcription	Aorta	Aorta
30	chr3:145924800-145935000	Weak transcription	HepG2	liver
31	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:145925600-145933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:145925600-145934600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
36	chr3:145927600-145938400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:145931400-145934600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:145932000-145934000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:145932000-145935600	Strong transcription	Liver	Liver
40	chr3:145932400-145936200	Strong transcription	Fetal Lung	lung
41	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:145932800-145934800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:145932800-145941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:145933200-145935800	Strong transcription	Adipose Nuclei	Adipose
45	chr3:145933400-145934200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:145933400-145934800	Strong transcription	HUVEC	blood vessel
47	chr3:145933400-145935000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:145933400-145935200	Strong transcription	Fetal Intestine Large	intestine
49	chr3:145933400-145935800	Strong transcription	Ovary	ovary
50	chr3:145933400-145935800	Strong transcription	Stomach Smooth Muscle	stomach

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