Variant report

Variant	rs3804656
Chromosome Location	chr3:145935163-145935164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11916269	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13062557	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063066	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064230	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13071899	0.92[ASN][1000 genomes]
rs13072399	0.92[ASN][1000 genomes]
rs13073749	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13082942	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13085381	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092543	0.92[ASN][1000 genomes]
rs13097291	0.85[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1398124	0.92[ASN][1000 genomes]
rs2175666	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175667	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34100380	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34286112	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34287919	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34363776	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34370775	0.92[ASN][1000 genomes]
rs34522376	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34901415	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34965829	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35054584	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35110814	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35231667	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35366505	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35403397	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35466414	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35632120	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35655354	0.92[ASN][1000 genomes]
rs35658240	0.92[ASN][1000 genomes]
rs35723694	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35969224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804655	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57375558	0.96[AFR][1000 genomes]
rs59405000	0.96[AFR][1000 genomes]
rs60949073	0.96[AFR][1000 genomes]
rs6766764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768389	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6782950	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71300385	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71300386	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71300388	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71300389	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71300390	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71300391	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73865353	0.96[AFR][1000 genomes]
rs73865355	0.96[AFR][1000 genomes]
rs73865357	0.96[AFR][1000 genomes]
rs73865364	0.96[AFR][1000 genomes]
rs73865365	0.96[AFR][1000 genomes]
rs73865368	0.96[AFR][1000 genomes]
rs73865369	0.96[AFR][1000 genomes]
rs73865370	0.96[AFR][1000 genomes]
rs73865378	0.96[AFR][1000 genomes]
rs73865384	0.96[AFR][1000 genomes]
rs73865386	0.96[AFR][1000 genomes]
rs73865392	0.88[AFR][1000 genomes]
rs73867526	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7614839	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642484	0.92[ASN][1000 genomes]
rs7652376	0.92[ASN][1000 genomes]

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:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145907000-145938600	Weak transcription	Fetal Intestine Small	intestine
2	chr3:145907600-145939200	Weak transcription	Brain Anterior Caudate	brain
3	chr3:145908200-145936400	Weak transcription	A549	lung
4	chr3:145909600-145939200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:145910400-145940000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:145913800-145939200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:145914200-145937000	Weak transcription	Placenta	Placenta
8	chr3:145914600-145940200	Weak transcription	Gastric	stomach
9	chr3:145914800-145940200	Weak transcription	Psoas Muscle	Psoas
10	chr3:145914800-145940400	Weak transcription	Spleen	Spleen
11	chr3:145917800-145940400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:145918000-145940400	Weak transcription	Pancreas	Pancrea
13	chr3:145918400-145940400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:145920600-145940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:145921600-145940200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:145922600-145940400	Weak transcription	Lung	lung
17	chr3:145924400-145939200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
20	chr3:145924600-145937200	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:145924600-145939000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:145924600-145940200	Weak transcription	Aorta	Aorta
23	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
26	chr3:145927600-145938400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:145932000-145935600	Strong transcription	Liver	Liver
28	chr3:145932400-145936200	Strong transcription	Fetal Lung	lung
29	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:145932800-145941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:145933200-145935800	Strong transcription	Adipose Nuclei	Adipose
32	chr3:145933400-145935200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:145933400-145935800	Strong transcription	Ovary	ovary
34	chr3:145933400-145935800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:145934000-145940400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:145934200-145939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:145934400-145935800	Enhancers	HMEC	breast
38	chr3:145934600-145935200	Weak transcription	NHLF	lung
39	chr3:145934600-145935600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:145934600-145935800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:145934600-145935800	Enhancers	Osteobl	bone
42	chr3:145934600-145936000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:145934600-145940200	Weak transcription	Fetal Stomach	stomach
44	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:145934800-145935200	Strong transcription	Left Ventricle	heart
46	chr3:145934800-145935200	Genic enhancers	HUVEC	blood vessel
47	chr3:145934800-145935400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:145934800-145935600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:145934800-145935600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:145934800-145935600	Enhancers	NHEK	skin

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