Variant report

Variant	rs9835958
Chromosome Location	chr3:78896598-78896599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:78887158..78889804-chr3:78895316..78898187,2	MCF-7	breast:
2	chr3:78896551..78898396-chr3:79065957..79069291,3	MCF-7	breast:
3	chr3:78896368..78899171-chr3:78904358..78907500,3	MCF-7	breast:
4	chr3:78878304..78880959-chr3:78895079..78897544,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169855	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12714473	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1383407	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[AMR][1000 genomes]
rs1480687	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480688	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162870	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs1843786	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs28629289	0.85[EUR][1000 genomes]
rs439325	0.88[CEU][hapmap]
rs444598	1.00[YRI][hapmap]
rs9309819	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs9309820	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs967454	1.00[YRI][hapmap]
rs9837982	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9861264	0.83[EUR][1000 genomes]
rs9863758	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs9875094	1.00[YRI][hapmap]
rs9877603	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs9881587	0.96[CEU][hapmap];0.85[EUR][1000 genomes]

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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78889400-78898800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:78889400-78899000	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:78892600-78897600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:78893600-78900000	Enhancers	HepG2	liver
5	chr3:78895000-78896800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:78895000-78897400	Weak transcription	Liver	Liver
7	chr3:78895400-78896600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:78895400-78897000	Enhancers	HMEC	breast
9	chr3:78895800-78896600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:78895800-78896600	Enhancers	NHLF	lung
11	chr3:78895800-78897000	Enhancers	HSMM	muscle
12	chr3:78895800-78897400	Enhancers	NHEK	skin
13	chr3:78896000-78896600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:78896000-78896600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:78896000-78896600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:78896000-78896600	Enhancers	Colon Smooth Muscle	Colon
17	chr3:78896000-78896600	Enhancers	Fetal Muscle Leg	muscle
18	chr3:78896000-78896600	Enhancers	HSMMtube	muscle
19	chr3:78896000-78896600	Enhancers	Osteobl	bone
20	chr3:78896000-78896800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:78896000-78896800	Enhancers	NH-A	brain
22	chr3:78896000-78897000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:78896000-78897200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:78896000-78897200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:78896000-78898200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:78896000-78899200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:78896200-78896600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:78896200-78896600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:78896200-78896600	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:78896200-78897600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:78896200-78897600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:78896200-78897600	Enhancers	A549	lung
33	chr3:78896200-78898200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:78896200-78898800	Weak transcription	Brain Substantia Nigra	brain
35	chr3:78896400-78896600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:78896400-78896600	Flanking Active TSS	Fetal Lung	lung
37	chr3:78896400-78897000	Enhancers	Fetal Stomach	stomach
38	chr3:78896400-78897800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:78896400-78899200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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