Variant report

Variant	rs3773236
Chromosome Location	chr3:78778901-78778902
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	chr3:78766178..78768497-chr3:78778226..78779744,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11127631	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11127632	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083361	0.84[EUR][1000 genomes]
rs13093540	0.86[EUR][1000 genomes]
rs1350366	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1386431	0.81[EUR][1000 genomes]
rs17016456	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2043661	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3773232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773244	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3926199	0.80[EUR][1000 genomes]
rs57373402	0.86[AMR][1000 genomes]
rs6807536	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809232	0.87[MKK][hapmap];0.82[TSI][hapmap]
rs7626082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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	esv1842222	chr3:78744206-78778901	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	esv3404191	chr3:78777462-78781660	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3499836	chr3:78778712-78780710	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78766600-78783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:78772000-78792200	Weak transcription	HepG2	liver
3	chr3:78774400-78783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:78777200-78779400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:78777200-78779400	Enhancers	Brain Germinal Matrix	brain
6	chr3:78777400-78779000	Enhancers	Fetal Lung	lung
7	chr3:78777400-78779400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:78777400-78780000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:78777400-78780400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:78777600-78780000	Enhancers	Fetal Brain Male	brain
11	chr3:78777800-78779000	Enhancers	Osteobl	bone
12	chr3:78777800-78779200	Enhancers	Fetal Stomach	stomach
13	chr3:78777800-78779400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:78777800-78779400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:78777800-78779400	Enhancers	Fetal Brain Female	brain
16	chr3:78777800-78780600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:78778000-78779000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:78778000-78779200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:78778000-78779400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:78778000-78779400	Enhancers	Colon Smooth Muscle	Colon
21	chr3:78778200-78779200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:78778200-78779200	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:78778200-78782800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:78778400-78779000	Enhancers	Brain Hippocampus Middle	brain
25	chr3:78778400-78779200	Enhancers	Adipose Nuclei	Adipose
26	chr3:78778400-78779600	Enhancers	Brain Angular Gyrus	brain
27	chr3:78778600-78779000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:78778600-78781600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:78778600-78783200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:78778800-78779800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:78778800-78779800	Weak transcription	NHDF-Ad	bronchial
32	chr3:78778800-78780600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:78778800-78783000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:78778800-78783400	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:78778800-78785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:78778800-78787200	Weak transcription	HSMM	muscle

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