Variant report

Variant	rs7752709
Chromosome Location	chr6:129042078-129042079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128840353..128841991-chr6:129041299..129043554,3	MCF-7	breast:
2	chr6:129041873..129044380-chr6:129047033..129049794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10485164	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12663546	0.89[ASN][1000 genomes]
rs1361592	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396299	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1396300	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1396301	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1396302	0.84[ASN][1000 genomes]
rs1396303	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1396304	0.84[ASN][1000 genomes]
rs1508437	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1508438	0.85[ASN][1000 genomes]
rs1508439	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1508440	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17056397	0.97[ASN][1000 genomes]
rs17056422	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2063207	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2064581	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2064582	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2064583	0.85[ASN][1000 genomes]
rs2064584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174934	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2326739	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2326740	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2326741	0.85[ASN][1000 genomes]
rs2326742	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2326743	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4457181	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs485179	0.83[ASN][1000 genomes]
rs4895837	0.85[ASN][1000 genomes]
rs4897270	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4897272	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897275	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs497668	0.83[ASN][1000 genomes]
rs506953	0.81[ASN][1000 genomes]
rs528060	0.80[ASN][1000 genomes]
rs529678	0.81[ASN][1000 genomes]
rs573382	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57744071	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61613152	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62425863	0.83[ASN][1000 genomes]
rs6569540	0.82[ASN][1000 genomes]
rs6569541	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6569542	0.84[ASN][1000 genomes]
rs6569543	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6569544	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6569545	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6569546	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6569547	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6569548	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6569549	0.87[ASN][1000 genomes]
rs6569550	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6569551	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6569552	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6569553	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569554	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899438	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6899472	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6899518	0.85[ASN][1000 genomes]
rs6899718	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6899904	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6911163	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911735	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911931	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919812	0.87[AFR][1000 genomes]
rs6919933	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6927434	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6933496	0.89[ASN][1000 genomes]
rs6934363	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934365	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935888	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6936447	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6937636	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6938304	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6938488	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6938701	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs774284	0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs774290	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774291	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744000	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748311	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748702	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753865	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754832	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757306	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7757503	0.81[ASN][1000 genomes]
rs7763313	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7768942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773822	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7775324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9321128	0.82[ASN][1000 genomes]
rs9321129	0.85[ASN][1000 genomes]
rs9372899	0.82[ASN][1000 genomes]
rs9372900	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9375587	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9375588	0.85[ASN][1000 genomes]
rs9375589	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9375590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385470	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9388659	0.83[ASN][1000 genomes]
rs9388662	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388663	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398879	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9402064	0.83[ASN][1000 genomes]
rs9402065	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9402066	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9402067	0.85[ASN][1000 genomes]
rs9402068	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9492049	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9492052	0.86[AFR][1000 genomes];0.85[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	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1030330	chr6:129008538-129095108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:129018600-129045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:129026600-129044000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:129040400-129042200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:129040800-129042200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:129040800-129042400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:129040800-129044800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:129040800-129047200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:129041000-129047200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:129041200-129042400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:129041400-129043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:129041600-129042200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:129041600-129042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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