Variant report

Variant	rs688058
Chromosome Location	chr3:101585467-101585468
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101580233..101583305-chr3:101583539..101587292,4	MCF-7	breast:
2	chr1:249145392..249145892-chr3:101584833..101585716,2	Hela-S3	cervix:
3	chr3:101566766..101570360-chr3:101584530..101589455,9	K562	blood:
4	chr3:101583187..101585591-chr3:101588676..101591535,3	MCF-7	breast:
5	chr3:101566766..101570360-chr3:101585005..101589455,7	K562	blood:

Variant related genes	Relation type
ENSG00000144802	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs14134	0.95[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2925332	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925333	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587555	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs592332	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592779	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599849	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs601225	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs618901	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622122	0.95[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs654219	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677011	0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs678354	0.93[ASW][hapmap];0.82[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs680508	0.82[ASN][1000 genomes]
rs681573	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101576400-101586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:101576400-101586800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:101576600-101586200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:101577200-101586200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:101579200-101586400	Weak transcription	Fetal Kidney	kidney
7	chr3:101579200-101586400	Weak transcription	K562	blood
8	chr3:101579400-101586200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:101579400-101586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:101579400-101586400	Weak transcription	Small Intestine	intestine
11	chr3:101579400-101586600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:101579400-101587200	Weak transcription	NHEK	skin
13	chr3:101579400-101587400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:101579400-101587600	Weak transcription	Aorta	Aorta
15	chr3:101579400-101587600	Weak transcription	Gastric	stomach
16	chr3:101579400-101587600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:101579400-101587800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:101579400-101588600	Weak transcription	Esophagus	oesophagus
19	chr3:101580000-101587400	Weak transcription	Fetal Lung	lung
20	chr3:101580400-101587600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:101580600-101586000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:101580800-101587400	Weak transcription	HMEC	breast
23	chr3:101580800-101587600	Weak transcription	Placenta	Placenta
24	chr3:101580800-101588600	Weak transcription	NHDF-Ad	bronchial
25	chr3:101581000-101586200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:101581000-101586400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:101581200-101586400	Weak transcription	Pancreas	Pancrea
28	chr3:101581200-101587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:101581200-101587400	Weak transcription	Primary B cells from cord blood	blood
30	chr3:101581200-101587600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:101581400-101586400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:101581400-101586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:101581400-101586400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:101581400-101586600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:101581400-101587200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:101581400-101587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:101581400-101587600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:101581600-101586200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:101581600-101587200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:101581600-101587400	Weak transcription	Adipose Nuclei	Adipose
41	chr3:101581600-101587600	Weak transcription	GM12878-XiMat	blood
42	chr3:101581800-101587000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:101581800-101587200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:101582000-101585600	Weak transcription	HSMM	muscle
45	chr3:101582000-101586000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:101582000-101586600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:101582000-101587000	Weak transcription	Left Ventricle	heart
48	chr3:101582000-101587200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:101582000-101587600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:101583200-101586000	Weak transcription	Fetal Heart	heart

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