Variant report

Variant	rs1477842
Chromosome Location	chr3:110894456-110894457
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11717706	0.82[AMR][1000 genomes]
rs11929280	0.85[CEU][hapmap]
rs13060876	0.80[AMR][1000 genomes]
rs13061640	0.80[AMR][1000 genomes]
rs13072462	0.82[AMR][1000 genomes]
rs13093206	0.81[AFR][1000 genomes]
rs1477841	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1477843	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs1477846	1.00[CEU][hapmap]
rs1477847	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs1477848	1.00[CEU][hapmap]
rs1477851	0.86[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1547518	0.82[AMR][1000 genomes]
rs2126713	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs2169643	0.85[CEU][hapmap]
rs2399373	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs2399375	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4682033	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4682034	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682229	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes]
rs4682230	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs4682231	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs4682234	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4682238	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4682240	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55774570	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56668317	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs57417964	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6437948	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6437952	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6437953	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6437955	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66803420	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67209183	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6786854	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794645	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7430600	1.00[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7433877	0.85[CEU][hapmap]
rs7610760	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7612572	0.82[AMR][1000 genomes]
rs7612667	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs7623847	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7623880	1.00[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7653595	1.00[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs873132	0.85[CEU][hapmap]
rs9288918	0.85[CEU][hapmap]
rs9821335	1.00[CEU][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes]
rs9828899	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs9866028	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9876350	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110832400-110911200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:110842600-110911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:110847000-110911400	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:110853000-110919600	Weak transcription	Fetal Brain Male	brain
6	chr3:110853200-110897000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:110853200-110911000	Weak transcription	NH-A	brain
8	chr3:110869400-110929000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:110871000-110914200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:110871200-110896400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:110872200-110913800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:110872600-110918800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:110872800-110896000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:110874200-110912000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:110874400-110911800	Weak transcription	Left Ventricle	heart
16	chr3:110874800-110913000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:110875200-110897600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:110880600-110903600	Weak transcription	Fetal Kidney	kidney
19	chr3:110881000-110928000	Weak transcription	Osteobl	bone
20	chr3:110883800-110908400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:110889000-110894600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:110890000-110894800	Strong transcription	HSMM	muscle
23	chr3:110890200-110913200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:110890800-110919800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:110892000-110895400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:110892000-110915800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:110892400-110903400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:110892400-110911200	Weak transcription	Liver	Liver
29	chr3:110892400-110912800	Weak transcription	HepG2	liver
30	chr3:110892800-110910000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:110892800-110911000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:110892800-110911000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:110892800-110911200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:110892800-110911600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:110893000-110910000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:110893000-110911400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:110893000-110916200	Weak transcription	A549	lung
38	chr3:110893200-110908000	Weak transcription	Placenta	Placenta
39	chr3:110893200-110912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:110893200-110912200	Weak transcription	NHDF-Ad	bronchial
41	chr3:110893400-110897800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:110893400-110911400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:110893600-110904000	Weak transcription	Fetal Lung	lung
44	chr3:110893800-110898400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:110893800-110903200	Weak transcription	Dnd41	blood
46	chr3:110893800-110903800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:110894000-110902800	Weak transcription	HSMMtube	muscle
48	chr3:110894000-110922800	Weak transcription	Gastric	stomach
49	chr3:110894000-110924000	Weak transcription	Fetal Stomach	stomach
50	chr3:110894000-110934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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