Variant report

Variant	rs6802139
Chromosome Location	chr3:135627433-135627434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135626053..135627736-chr3:135684595..135686166,2	MCF-7	breast:
2	chr3:135625811..135627915-chr3:135682871..135685242,3	MCF-7	breast:
3	chr3:135625715..135628669-chr3:135629036..135632014,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap]
rs10512973	1.00[CHB][hapmap]
rs10512981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935175	1.00[JPT][hapmap]
rs13072596	0.93[ASN][1000 genomes]
rs13097946	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13098245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13322891	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13325914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13434196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356664	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1401545	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403766	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403767	0.85[ASN][1000 genomes]
rs1403770	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1523595	0.93[ASN][1000 genomes]
rs1523596	0.93[ASN][1000 genomes]
rs1523597	0.93[ASN][1000 genomes]
rs1568349	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568350	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17196987	0.93[ASN][1000 genomes]
rs17197552	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17250445	0.86[ASN][1000 genomes]
rs2204259	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570106	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28855968	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28875187	0.85[ASN][1000 genomes]
rs34311570	0.86[ASN][1000 genomes]
rs35257855	0.86[ASN][1000 genomes]
rs35722356	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073308	0.81[CEU][hapmap];0.93[ASN][1000 genomes]
rs4718	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55678980	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56308637	0.85[ASN][1000 genomes]
rs56807950	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59063369	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66544356	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67039922	0.93[ASN][1000 genomes]
rs6771224	0.93[ASN][1000 genomes]
rs6771997	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6773469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774289	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6775778	1.00[JPT][hapmap]
rs6779603	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786769	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6803447	1.00[CHB][hapmap]
rs6807058	1.00[JPT][hapmap]
rs6807242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6809006	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6810223	0.93[ASN][1000 genomes]
rs7433567	0.82[CEU][hapmap]
rs7609938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621331	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621396	1.00[JPT][hapmap]
rs7621425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7626676	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640153	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs870812	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs908825	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9289502	0.93[ASN][1000 genomes]
rs9289503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9808979	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9812561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9813082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814505	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814557	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9819440	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9819988	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820189	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825239	1.00[JPT][hapmap]
rs9826806	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9829329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833470	1.00[CHB][hapmap]
rs9833699	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834104	0.93[ASN][1000 genomes]
rs9834624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836374	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9836758	1.00[JPT][hapmap]
rs9837855	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9843725	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9844478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846137	0.83[CEU][hapmap];0.93[ASN][1000 genomes]
rs9848322	1.00[JPT][hapmap]
rs9849088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851361	0.93[ASN][1000 genomes]
rs9853577	1.00[JPT][hapmap]
rs9854494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9862743	0.80[ASN][1000 genomes]
rs9862763	0.93[ASN][1000 genomes]
rs9864247	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9864514	0.93[ASN][1000 genomes]
rs9864656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864775	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9868246	0.83[CEU][hapmap];0.93[ASN][1000 genomes]
rs9870581	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9872542	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9875328	0.93[ASN][1000 genomes]
rs9875948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9876837	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877082	0.93[ASN][1000 genomes]
rs9877722	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9880721	0.93[ASN][1000 genomes]
rs9883808	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135625600-135628200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:135626000-135627800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:135626200-135628200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:135626400-135627600	Flanking Active TSS	NHEK	skin
5	chr3:135626400-135627800	Enhancers	Placenta	Placenta
6	chr3:135627000-135627600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:135627000-135627600	Enhancers	Pancreas	Pancrea
8	chr3:135627200-135627600	Enhancers	Lung	lung
9	chr3:135627200-135628000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:135627400-135627600	Enhancers	Gastric	stomach
11	chr3:135627400-135627800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:135627400-135627800	Enhancers	Esophagus	oesophagus
13	chr3:135627400-135628000	Enhancers	HMEC	breast
14	chr3:135627400-135629800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:135627400-135630200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:135627400-135632000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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