Variant report

Variant	rs329805
Chromosome Location	chr3:78929600-78929601
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78753197..78755809-chr3:78927184..78929667,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs13075210	0.84[CHB][hapmap]
rs1355983	0.81[CHB][hapmap]
rs1487135	0.88[CHB][hapmap]
rs162262	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162263	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs162264	0.87[CHB][hapmap]
rs162265	0.85[CHB][hapmap]
rs162266	0.83[EUR][1000 genomes]
rs162267	0.82[EUR][1000 genomes]
rs162268	0.93[CHB][hapmap];0.81[EUR][1000 genomes]
rs162423	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs162425	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs162426	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs162427	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17311057	0.86[CHB][hapmap]
rs17311169	0.87[CHB][hapmap]
rs17313732	0.81[CHB][hapmap]
rs1825760	0.88[CHB][hapmap]
rs1865861	0.80[CHB][hapmap]
rs1865863	0.81[CHB][hapmap]
rs186648	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs186688	0.87[CHB][hapmap]
rs2018432	0.88[CHB][hapmap]
rs2082973	0.88[CHB][hapmap]
rs328045	0.87[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs328047	0.93[CHB][hapmap]
rs329811	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329812	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs329813	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs329814	0.93[CHB][hapmap]
rs329815	0.82[EUR][1000 genomes]
rs329816	0.87[CHB][hapmap];0.85[EUR][1000 genomes]
rs329817	0.82[EUR][1000 genomes]
rs329818	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs329819	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329820	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329821	0.88[ASN][1000 genomes]
rs329822	0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329824	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs329825	0.85[CHB][hapmap]
rs331134	0.85[CHB][hapmap]
rs331139	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331143	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331145	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331149	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331158	0.91[CEU][hapmap];0.93[CHB][hapmap]
rs331161	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331162	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331163	0.90[EUR][1000 genomes]
rs331164	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331181	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331182	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331184	0.84[EUR][1000 genomes]
rs331188	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331189	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331190	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331199	0.83[CEU][hapmap];0.93[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs333483	0.87[CHB][hapmap]
rs333493	0.87[CHB][hapmap]
rs333507	0.87[CHB][hapmap]
rs369346	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs379346	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs387900	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs388421	0.85[ASN][1000 genomes]
rs432141	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs453354	0.83[EUR][1000 genomes]
rs4681013	0.91[CEU][hapmap];0.93[CHB][hapmap]
rs479956	0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs484531	0.85[ASN][1000 genomes]
rs498805	0.87[CEU][hapmap];0.93[CHB][hapmap];0.80[EUR][1000 genomes]
rs512135	0.80[EUR][1000 genomes]
rs531125	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6548600	0.85[CHB][hapmap]
rs6548601	0.94[CHB][hapmap]
rs6770452	0.87[CHB][hapmap]
rs6772919	0.94[CHB][hapmap]
rs6800782	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs7610996	0.88[CHB][hapmap]
rs7617433	0.86[CHB][hapmap]
rs7617538	0.80[CEU][hapmap];0.93[CHB][hapmap]
rs7619765	0.80[EUR][1000 genomes]
rs7629522	0.87[CHB][hapmap]
rs7650002	0.87[CHB][hapmap]
rs9866912	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590735	chr3:78922852-78977507	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78918000-78929800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:78921600-78936000	Weak transcription	HSMM	muscle
3	chr3:78921600-78936600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:78922000-78929800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:78922600-78944000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:78923000-78943800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:78925000-78930800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:78925200-78929600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:78925200-78929800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:78927000-78930000	Enhancers	NHDF-Ad	bronchial
11	chr3:78927000-78930600	Enhancers	HepG2	liver
12	chr3:78927400-78936400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:78927600-78929800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:78927600-78929800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:78927600-78930200	Weak transcription	Aorta	Aorta
16	chr3:78927600-78943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:78927800-78936200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:78928200-78929800	Enhancers	Brain Substantia Nigra	brain
19	chr3:78928200-78930000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:78928200-78931800	Enhancers	Fetal Brain Male	brain
21	chr3:78928400-78929800	Enhancers	Brain Hippocampus Middle	brain
22	chr3:78928400-78930200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:78928400-78930600	Enhancers	Brain Germinal Matrix	brain
24	chr3:78928400-78930800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:78928400-78931600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:78928600-78929600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:78928600-78930400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:78928800-78929600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:78928800-78929600	Weak transcription	Fetal Lung	lung
30	chr3:78928800-78929800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:78928800-78930000	Enhancers	Adipose Nuclei	Adipose
32	chr3:78928800-78930000	Enhancers	NHLF	lung
33	chr3:78928800-78930200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:78928800-78930400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr3:78928800-78930800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:78929000-78929600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:78929000-78930000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:78929000-78930000	Weak transcription	Fetal Stomach	stomach
39	chr3:78929000-78930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:78929000-78930400	Enhancers	Fetal Brain Female	brain
41	chr3:78929200-78929600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:78929400-78929800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:78929400-78929800	Weak transcription	Brain Angular Gyrus	brain
44	chr3:78929400-78930000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:78929400-78930400	Enhancers	Fetal Heart	heart
46	chr3:78929400-78930400	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:78929400-78936400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:78929600-78929800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:78929600-78929800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:78929600-78929800	Enhancers	Brain Cingulate Gyrus	brain

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