Variant report

Variant	rs329812
Chromosome Location	chr3:78904516-78904517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78896368..78899171-chr3:78904358..78907500,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1487135	0.86[CHB][hapmap]
rs162262	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162263	0.82[CEU][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap]
rs162265	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs162423	0.84[CEU][hapmap]
rs162425	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162426	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162427	0.95[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs162428	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes]
rs162429	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs17311057	0.84[CHB][hapmap]
rs17311169	0.86[CHB][hapmap]
rs1825760	0.86[CHB][hapmap]
rs2018432	0.86[CHB][hapmap]
rs2082973	0.86[CHB][hapmap]
rs328045	0.82[CEU][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap]
rs329805	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs329811	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs329813	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs329814	0.84[TSI][hapmap]
rs329819	0.91[CEU][hapmap];0.87[CHB][hapmap]
rs329824	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs329825	0.83[CHB][hapmap]
rs331134	0.82[CEU][hapmap]
rs331139	0.87[EUR][1000 genomes]
rs331143	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331145	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331149	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331158	0.95[CEU][hapmap];0.81[AMR][1000 genomes]
rs331161	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs331162	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs331163	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs331164	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331182	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331188	0.84[EUR][1000 genomes]
rs331190	0.81[EUR][1000 genomes]
rs331199	0.82[CEU][hapmap]
rs333483	0.85[CHB][hapmap]
rs333493	0.86[CHB][hapmap]
rs333507	0.86[CHB][hapmap]
rs432141	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681013	0.95[CEU][hapmap]
rs479956	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs498805	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs531125	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6548600	0.82[CHB][hapmap]
rs6770452	0.86[CHB][hapmap]
rs6800782	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs7610996	0.86[CHB][hapmap]
rs7617433	0.85[CHB][hapmap];0.80[GIH][hapmap]
rs7629522	0.86[CHB][hapmap]
rs7650002	0.85[CHB][hapmap]
rs9866912	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78896600-78908400	Weak transcription	Osteobl	bone
2	chr3:78897200-78907200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:78898200-78905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:78898600-78906800	Weak transcription	A549	lung
5	chr3:78899200-78906800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:78900800-78906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:78904000-78904800	Enhancers	HUVEC	blood vessel
8	chr3:78904200-78904600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:78904200-78904600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:78904200-78904600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:78904200-78904600	Enhancers	Fetal Kidney	kidney
12	chr3:78904200-78904600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:78904200-78904600	Enhancers	Spleen	Spleen
14	chr3:78904200-78904600	Enhancers	HSMMtube	muscle
15	chr3:78904200-78904800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:78904200-78904800	Enhancers	Colon Smooth Muscle	Colon
17	chr3:78904200-78904800	Enhancers	HSMM	muscle
18	chr3:78904200-78905000	Enhancers	Fetal Lung	lung
19	chr3:78904200-78905000	Enhancers	HepG2	liver
20	chr3:78904200-78905000	Enhancers	NHEK	skin
21	chr3:78904200-78905800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:78904400-78904600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr3:78904400-78904600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:78904400-78904800	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:78904400-78905000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:78904400-78905000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:78904400-78905400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:78904400-78906800	Weak transcription	Rectal Smooth Muscle	rectum

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