Variant report

Variant	rs6792259
Chromosome Location	chr3:142301439-142301440
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	chr3:142301410-142301458	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142296660..142299430-chr3:142300614..142303082,3	MCF-7	breast:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10935465	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1129393	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061823	0.91[CHB][hapmap]
rs13065075	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067795	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069307	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079246	0.82[CEU][hapmap]
rs13085998	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093869	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13098343	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357529	0.84[EUR][1000 genomes]
rs1357530	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs16852486	0.81[CEU][hapmap]
rs1916639	0.86[EUR][1000 genomes]
rs1983434	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1983435	0.86[EUR][1000 genomes]
rs2030613	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2049325	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2049326	0.87[EUR][1000 genomes]
rs2140432	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2177396	0.87[EUR][1000 genomes]
rs2227928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227930	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2354860	0.85[EUR][1000 genomes]
rs28617475	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2862743	0.91[CHB][hapmap]
rs2883380	0.81[CEU][hapmap]
rs3922730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4273389	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413348	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs4441672	0.92[CHB][hapmap]
rs4597728	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683688	0.81[CEU][hapmap]
rs4683690	0.82[CEU][hapmap]
rs6414350	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440082	0.91[CHB][hapmap]
rs6440086	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440087	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440088	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440090	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440091	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440092	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440093	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440098	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6440099	0.86[EUR][1000 genomes]
rs6768093	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770155	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772400	0.92[CHB][hapmap]
rs6775583	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775718	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6775813	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs6780250	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783203	0.86[EUR][1000 genomes]
rs6784089	0.86[EUR][1000 genomes]
rs6785675	0.86[EUR][1000 genomes]
rs6789958	0.81[CEU][hapmap]
rs6791816	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793735	0.81[CEU][hapmap]
rs6798232	0.81[CEU][hapmap]
rs6799752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802734	0.82[EUR][1000 genomes]
rs6802774	0.82[EUR][1000 genomes]
rs6808205	0.81[CEU][hapmap]
rs7428496	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430429	0.81[CEU][hapmap]
rs7609842	0.81[EUR][1000 genomes]
rs7610557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615316	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7623524	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630130	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631313	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7634158	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7635146	0.86[EUR][1000 genomes]
rs7641330	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646880	0.87[EUR][1000 genomes]
rs7647573	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7651071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7651542	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9683085	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808914	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808943	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9820353	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820770	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9824176	0.81[EUR][1000 genomes]
rs9824893	0.87[EUR][1000 genomes]
rs9825207	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826786	0.86[CHB][hapmap]
rs9828178	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9832606	0.82[CEU][hapmap]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap]
rs9855140	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9855919	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862919	0.91[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs9866958	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs9869842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876254	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9879995	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882763	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142301800	Weak transcription	Left Ventricle	heart
2	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:142298400-142306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:142298800-142305600	Weak transcription	Liver	Liver
6	chr3:142298800-142305600	Weak transcription	A549	lung
7	chr3:142299000-142303000	Weak transcription	K562	blood
8	chr3:142300600-142305600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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