Variant report

Variant	rs2118067
Chromosome Location	chr3:78764656-78764657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:78764560-78764710	GM12865	blood:	n/a	n/a
2	POLR2A	chr3:78764647-78764688	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ROBO1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10865570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11708898	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927671	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2043662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164549	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255164	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2608023	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2684377	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28429251	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681009	0.80[ASN][1000 genomes]
rs6769521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6785152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619742	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7631285	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs967454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9834909	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837496	1.00[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs984138	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9842948	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9856624	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864412	0.84[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9875094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78733800-78778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:78735200-78765600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:78740400-78773800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:78747000-78777400	Weak transcription	Fetal Heart	heart
5	chr3:78749000-78765800	Weak transcription	Ovary	ovary
6	chr3:78749600-78765600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:78752200-78773600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:78752600-78771000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:78753200-78765800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:78753600-78777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:78754000-78765000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:78754000-78772200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:78756200-78765800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:78756200-78773800	Weak transcription	Fetal Kidney	kidney
15	chr3:78756800-78777800	Weak transcription	Osteobl	bone
16	chr3:78757000-78765600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:78757000-78771000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:78757200-78765400	Weak transcription	Fetal Stomach	stomach
19	chr3:78757200-78765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:78757200-78768400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:78757200-78773800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:78757200-78775000	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:78758600-78765800	Weak transcription	HepG2	liver
24	chr3:78761200-78765800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:78761200-78777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:78761400-78777400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:78761400-78777600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:78762600-78765600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:78762600-78772800	Weak transcription	Brain Anterior Caudate	brain
30	chr3:78762800-78765200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:78762800-78774000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:78763000-78765600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:78763000-78765600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:78763000-78772600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:78763200-78765400	Weak transcription	Primary T cells from cord blood	blood
36	chr3:78763600-78765200	Weak transcription	Adipose Nuclei	Adipose
37	chr3:78763600-78773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:78764000-78765200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:78764000-78765600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:78764000-78765600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:78764200-78765200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:78764200-78771000	Weak transcription	Fetal Lung	lung
43	chr3:78764200-78777400	Weak transcription	Brain Angular Gyrus	brain
44	chr3:78764400-78766000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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