Variant report

Variant	rs7752593
Chromosome Location	chr6:79948648-79948649
allele	A/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	POLR2A	chr6:79948514-79948826	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr6:79948627-79949067	MCF-7	breast:	n/a	chr6:79948860-79948871
3	CEBPB	chr6:79948634-79949561	Hela-S3	cervix:	n/a	chr6:79948860-79948871
4	TCF7L2	chr6:79948492-79949478	Hela-S3	cervix:	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
ENSG00000146247	Chromatin interaction
ENSG00000118418	Chromatin interaction
ENSG00000270362	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10455359	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10806163	0.86[EUR][1000 genomes]
rs11965180	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11966786	1.00[EUR][1000 genomes]
rs11969279	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12194892	0.86[EUR][1000 genomes]
rs12209677	0.86[EUR][1000 genomes]
rs1335535	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1335537	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1335538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1414279	0.86[EUR][1000 genomes]
rs1414283	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1414284	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1537739	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1537740	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1582079	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16890450	0.86[EUR][1000 genomes]
rs1832088	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1832089	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1889685	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2065749	0.86[AFR][1000 genomes]
rs2065750	0.90[AFR][1000 genomes]
rs2095633	0.92[EUR][1000 genomes]
rs2322216	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs2322219	0.97[EUR][1000 genomes]
rs2874732	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2874733	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3934335	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4112504	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4235810	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4301272	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4377755	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4407672	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4418150	0.85[CEU][hapmap];0.97[EUR][1000 genomes]
rs4432946	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4464749	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4470813	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4537102	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4555887	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706754	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4706755	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4706756	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4706759	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4706760	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706766	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55635444	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56183421	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56193084	0.86[EUR][1000 genomes]
rs56354335	0.86[EUR][1000 genomes]
rs56955811	0.86[EUR][1000 genomes]
rs57340384	1.00[EUR][1000 genomes]
rs57608966	0.86[EUR][1000 genomes]
rs59152048	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59858042	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61227507	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61558200	0.86[EUR][1000 genomes]
rs62411290	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6454106	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907042	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907264	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6913297	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6917165	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs6924790	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6929660	0.97[EUR][1000 genomes]
rs6941433	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73468020	0.89[EUR][1000 genomes]
rs73468035	0.86[EUR][1000 genomes]
rs73767530	0.86[EUR][1000 genomes]
rs7738508	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7739118	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7746915	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7751974	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7757062	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7760458	1.00[EUR][1000 genomes]
rs7760939	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7763232	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7764517	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770245	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7772967	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9341765	0.81[AFR][1000 genomes]
rs9343886	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9343890	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9350803	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9352710	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9359369	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs9361504	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9361511	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9443654	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79944400-79948800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:79944400-79950400	Weak transcription	Lung	lung
3	chr6:79944800-79948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:79944800-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:79944800-79948800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:79944800-79949200	Weak transcription	HMEC	breast
7	chr6:79944800-79950400	Weak transcription	Right Ventricle	heart
8	chr6:79945000-79948800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:79945000-79948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:79945000-79949000	Weak transcription	Psoas Muscle	Psoas
11	chr6:79945000-79955400	Weak transcription	Aorta	Aorta
12	chr6:79947600-79949000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:79947600-79949200	Enhancers	GM12878-XiMat	blood
14	chr6:79947800-79950800	Enhancers	Hela-S3	cervix
15	chr6:79948400-79949000	Enhancers	Fetal Heart	heart
16	chr6:79948400-79949200	Enhancers	HepG2	liver
17	chr6:79948400-79949400	Enhancers	Left Ventricle	heart
18	chr6:79948600-79949000	Enhancers	Liver	Liver
19	chr6:79948600-79949200	Enhancers	Fetal Intestine Small	intestine
20	chr6:79948600-79949200	Enhancers	Ovary	ovary
21	chr6:79948600-79949400	Enhancers	Pancreas	Pancrea
22	chr6:79948600-79949400	Enhancers	Right Atrium	heart
23	chr6:79948600-79949400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:79948600-79949400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr6:79948600-79949600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:79948600-79949600	Enhancers	Stomach Mucosa	stomach
27	chr6:79948600-79949600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:79948600-79949800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:79948600-79949800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:79948600-79950000	Enhancers	Placenta	Placenta
31	chr6:79948600-79950000	Enhancers	NHEK	skin

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