Variant report

Variant	rs4706759
Chromosome Location	chr6:79947273-79947274
allele	C/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	POLR2A	chr6:79947184-79947317	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79943151..79946532-chr6:79946546..79950345,4	MCF-7	breast:
3	chr6:79943641..79946431-chr6:79946623..79949895,4	MCF-7	breast:

Variant related genes	Relation type
HMGN3	TF binding region
ENSG00000270362	Chromatin interaction
ENSG00000146247	Chromatin interaction
ENSG00000118418	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10455359	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11965180	0.87[EUR][1000 genomes]
rs11966786	0.90[EUR][1000 genomes]
rs11969279	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1335535	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1335537	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1335538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1414283	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1414284	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1537739	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1537740	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1582079	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1832088	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1832089	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1889685	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2065749	0.82[AFR][1000 genomes]
rs2065750	0.86[AFR][1000 genomes]
rs2095633	0.82[EUR][1000 genomes]
rs2322216	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs2322219	0.87[EUR][1000 genomes]
rs2874732	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2874733	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3934335	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4112504	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4235810	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4301272	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4377755	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4407672	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4418150	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4432946	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4464749	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4470813	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4537102	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4555887	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4706754	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4706755	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4706756	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4706760	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4706765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4706766	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55635444	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56183421	0.87[EUR][1000 genomes]
rs57340384	0.90[EUR][1000 genomes]
rs59152048	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59858042	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61227507	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62411290	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6454106	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6907042	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6907264	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6913297	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6917165	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs6924790	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6929660	0.87[EUR][1000 genomes]
rs6941433	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7738508	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7739118	0.87[EUR][1000 genomes]
rs7746915	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7751974	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7752593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7757062	0.87[EUR][1000 genomes]
rs7760458	0.90[EUR][1000 genomes]
rs7760939	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7763232	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7764517	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7770245	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7772967	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9343886	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9343890	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9350803	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9352710	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9359369	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs9361504	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9361511	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9443654	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs989191	0.80[YRI][hapmap]

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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79944400-79948400	Weak transcription	Left Ventricle	heart
2	chr6:79944400-79948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:79944400-79948600	Weak transcription	Stomach Mucosa	stomach
4	chr6:79944400-79948800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:79944400-79950400	Weak transcription	Lung	lung
6	chr6:79944600-79948600	Weak transcription	Ovary	ovary
7	chr6:79944600-79948600	Weak transcription	Pancreas	Pancrea
8	chr6:79944600-79948600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:79944800-79947400	Weak transcription	NH-A	brain
10	chr6:79944800-79947600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:79944800-79947600	Weak transcription	GM12878-XiMat	blood
12	chr6:79944800-79948600	Weak transcription	Liver	Liver
13	chr6:79944800-79948600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:79944800-79948600	Weak transcription	Fetal Intestine Small	intestine
15	chr6:79944800-79948600	Weak transcription	Right Atrium	heart
16	chr6:79944800-79948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:79944800-79948600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:79944800-79948600	Weak transcription	NHEK	skin
19	chr6:79944800-79948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:79944800-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:79944800-79948800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:79944800-79949200	Weak transcription	HMEC	breast
23	chr6:79944800-79950400	Weak transcription	Right Ventricle	heart
24	chr6:79945000-79947800	Weak transcription	Hela-S3	cervix
25	chr6:79945000-79948400	Weak transcription	Fetal Heart	heart
26	chr6:79945000-79948400	Weak transcription	HepG2	liver
27	chr6:79945000-79948600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:79945000-79948600	Weak transcription	Placenta	Placenta
29	chr6:79945000-79948800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:79945000-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:79945000-79949000	Weak transcription	Psoas Muscle	Psoas
32	chr6:79945000-79955400	Weak transcription	Aorta	Aorta
33	chr6:79946800-79947600	Weak transcription	Fetal Thymus	thymus

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