Variant report

Variant	rs6786110
Chromosome Location	chr3:177649280-177649281
allele	A/G
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	TCF12	chr3:177648932-177649804	SK-N-SH	brain:	n/a	n/a
2	MEF2A	chr3:177649022-177649605	SK-N-SH	brain:	n/a	chr3:177649396-177649412 chr3:177649397-177649411 chr3:177649395-177649416 chr3:177649399-177649410 chr3:177649395-177649416 chr3:177649396-177649411 chr3:177649397-177649412
3	FOS	chr3:177649197-177649460	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr3:177648927-177649703	SK-N-SH	brain:	n/a	chr3:177649427-177649436
5	PBX3	chr3:177649007-177649620	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr3:177649041-177649638	SK-N-SH	brain:	n/a	n/a
7	JUND	chr3:177649069-177649621	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:177649208-177649488	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr3:177648919-177649669	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr3:177649187-177649589	SK-N-SH	brain:	n/a	n/a
11	MEF2A	chr3:177648927-177649705	SK-N-SH	brain:	n/a	chr3:177649396-177649412 chr3:177649397-177649411 chr3:177649395-177649416 chr3:177649399-177649410 chr3:177649619-177649635 chr3:177649395-177649416 chr3:177649396-177649411 chr3:177649397-177649412
12	GATA3	chr3:177648750-177649799	SK-N-SH	brain:	n/a	n/a
13	FOS	chr3:177649269-177649521	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr3:177648358-177649864	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr3:177649063-177649697	SK-N-SH	brain:	n/a	n/a
16	NFIC	chr3:177648883-177649603	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr3:177648776-177649739	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000225790	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1075544	0.95[ASN][1000 genomes]
rs10936960	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11919677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920776	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11922170	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489750	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492069	0.83[ASN][1000 genomes]
rs12492409	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496207	0.89[ASN][1000 genomes]
rs12497387	0.80[ASN][1000 genomes]
rs13062823	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13066104	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs13075342	0.80[ASN][1000 genomes]
rs13087011	0.94[ASN][1000 genomes]
rs13314585	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1362828	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362829	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1421157	0.95[ASN][1000 genomes]
rs1421158	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1421160	0.92[ASN][1000 genomes]
rs1421161	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1421162	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1421166	0.91[ASN][1000 genomes]
rs1421167	0.91[ASN][1000 genomes]
rs1421169	0.82[ASN][1000 genomes]
rs1421170	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421173	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16828811	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs16828819	0.81[ASN][1000 genomes]
rs1861886	0.83[ASN][1000 genomes]
rs1895068	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1895072	0.84[ASN][1000 genomes]
rs1895073	0.83[ASN][1000 genomes]
rs1895074	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895075	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2160836	0.84[ASN][1000 genomes]
rs34300091	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34534264	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34969108	0.84[ASN][1000 genomes]
rs35494413	0.84[ASN][1000 genomes]
rs35569214	0.84[ASN][1000 genomes]
rs35751119	0.82[ASN][1000 genomes]
rs3961634	0.84[ASN][1000 genomes]
rs3978728	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57315928	0.95[ASN][1000 genomes]
rs6769109	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6775970	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6776256	0.82[ASN][1000 genomes]
rs6779965	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783796	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6804905	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6807952	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6808901	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs737553	0.95[ASN][1000 genomes]
rs737555	0.94[ASN][1000 genomes]
rs7616735	0.80[EUR][1000 genomes]
rs7619802	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7645977	0.93[ASN][1000 genomes]
rs7648771	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9830203	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9838142	0.95[ASN][1000 genomes]
rs9862300	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9875424	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177638000-177649800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:177645600-177652000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:177646400-177651000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:177646600-177649800	Weak transcription	A549	lung
5	chr3:177646600-177649800	Weak transcription	NH-A	brain
6	chr3:177646600-177650400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:177646800-177652000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:177647200-177650400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:177647200-177650400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:177647200-177651200	Weak transcription	HSMMtube	muscle
11	chr3:177647400-177650200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:177648000-177652400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:177648000-177652400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:177648200-177650400	Enhancers	HMEC	breast
15	chr3:177648200-177650800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:177648200-177655000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:177648400-177652800	Enhancers	Osteobl	bone
18	chr3:177648400-177653000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:177648600-177651800	Weak transcription	Fetal Heart	heart
20	chr3:177648600-177652400	Enhancers	Brain Germinal Matrix	brain
21	chr3:177648600-177652600	Enhancers	HSMM	muscle
22	chr3:177648600-177652600	Enhancers	NHDF-Ad	bronchial
23	chr3:177648800-177649400	Enhancers	Psoas Muscle	Psoas
24	chr3:177648800-177650400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:177648800-177650400	Enhancers	Adipose Nuclei	Adipose
26	chr3:177648800-177650800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:177648800-177652600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:177649000-177649400	Enhancers	Right Atrium	heart
29	chr3:177649000-177650200	Weak transcription	Fetal Lung	lung
30	chr3:177649000-177652200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:177649200-177650000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:177649200-177650200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:177649200-177651200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:177649200-177651200	Weak transcription	NHLF	lung
35	chr3:177649200-177651800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:177649200-177652600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:177649200-177657000	Weak transcription	Esophagus	oesophagus

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