Variant report

Variant	rs11927671
Chromosome Location	chr3:78787869-78787870
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78787390..78790233-chr3:78791850..78793816,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10865570	0.92[CEU][hapmap]
rs11708898	0.85[EUR][1000 genomes]
rs11714414	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2043662	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2118067	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2164549	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2255164	0.84[CEU][hapmap]
rs2608023	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28429251	0.86[EUR][1000 genomes]
rs28482804	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs56315536	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6769521	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6785152	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7619742	0.92[CEU][hapmap]
rs967454	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9834909	0.87[EUR][1000 genomes]
rs9837496	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs984138	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9842948	0.81[EUR][1000 genomes]
rs9856624	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9864412	0.96[CEU][hapmap]
rs9874934	0.82[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9875094	0.92[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2753211	chr3:78784269-78809116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78772000-78792200	Weak transcription	HepG2	liver
2	chr3:78783200-78797000	Weak transcription	Fetal Lung	lung
3	chr3:78783800-78803400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:78786800-78788200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:78787000-78788000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:78787000-78788000	Enhancers	Osteobl	bone
7	chr3:78787000-78788400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:78787000-78788400	Enhancers	HUVEC	blood vessel
9	chr3:78787200-78788000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:78787200-78788000	Enhancers	Fetal Brain Male	brain
11	chr3:78787200-78788800	Enhancers	NH-A	brain
12	chr3:78787400-78788000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:78787400-78788000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:78787400-78791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:78787400-78802800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:78787400-78814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:78787600-78791200	Weak transcription	Fetal Brain Female	brain
18	chr3:78787600-78792600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:78787600-78794200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:78787800-78791800	Weak transcription	HSMM	muscle
21	chr3:78787800-78800000	Weak transcription	HMEC	breast

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