Variant report

Variant	rs1523597
Chromosome Location	chr3:135739722-135739723
allele	A/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	E2F4	chr3:135739552-135739846	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr3:135739544-135739744	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135716831..135719194-chr3:135738292..135740205,2	MCF-7	breast:

Variant related genes	Relation type
PPP2R3A	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10048942	0.84[ASN][1000 genomes]
rs10049233	0.84[ASN][1000 genomes]
rs10512981	0.93[ASN][1000 genomes]
rs10935175	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072596	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082684	0.84[ASN][1000 genomes]
rs13097946	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098245	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	0.93[ASN][1000 genomes]
rs1403766	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1403770	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568349	0.93[ASN][1000 genomes]
rs16843509	0.93[ASN][1000 genomes]
rs17196987	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197552	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250445	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.93[ASN][1000 genomes]
rs28449384	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28576629	0.84[ASN][1000 genomes]
rs34311570	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34409306	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34522617	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34767379	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35257855	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36039354	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073308	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56807950	0.93[ASN][1000 genomes]
rs59063369	0.93[ASN][1000 genomes]
rs66544356	0.93[ASN][1000 genomes]
rs67039922	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771224	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771997	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773469	0.93[ASN][1000 genomes]
rs6774289	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	0.84[ASN][1000 genomes]
rs6779603	0.93[ASN][1000 genomes]
rs6786769	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802139	0.93[ASN][1000 genomes]
rs6807058	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807242	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807565	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810223	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336046	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73222222	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427833	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7433567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609938	0.93[ASN][1000 genomes]
rs7621331	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621396	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621425	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626676	0.93[ASN][1000 genomes]
rs7628848	0.84[ASN][1000 genomes]
rs7638129	0.93[ASN][1000 genomes]
rs7640153	0.93[ASN][1000 genomes]
rs7641070	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7643661	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808979	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812561	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813082	0.93[ASN][1000 genomes]
rs9814557	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819988	0.93[ASN][1000 genomes]
rs9824558	0.93[ASN][1000 genomes]
rs9825239	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9826806	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829329	0.93[ASN][1000 genomes]
rs9829476	0.93[ASN][1000 genomes]
rs9833799	0.93[ASN][1000 genomes]
rs9834104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836374	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836758	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837355	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9839259	0.93[ASN][1000 genomes]
rs9842840	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842864	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843725	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844478	0.93[ASN][1000 genomes]
rs9846137	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848322	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849088	0.93[ASN][1000 genomes]
rs9851361	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853577	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9862264	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862743	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862763	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864247	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864514	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864656	0.93[ASN][1000 genomes]
rs9868246	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872542	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875328	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876837	0.93[ASN][1000 genomes]
rs9877082	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880721	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	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
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135707000-135741600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:135717200-135747000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:135718000-135753000	Weak transcription	Fetal Kidney	kidney
4	chr3:135719000-135741600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:135719200-135746200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:135726200-135748000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:135726400-135758400	Weak transcription	Lung	lung
9	chr3:135727200-135746600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:135727400-135760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:135727800-135741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:135727800-135741600	Weak transcription	Pancreas	Pancrea
13	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:135728000-135748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:135728200-135746400	Weak transcription	Ovary	ovary
16	chr3:135735600-135741600	Enhancers	Fetal Heart	heart
17	chr3:135735800-135760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:135737000-135740000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:135737200-135739800	Enhancers	NHDF-Ad	bronchial
20	chr3:135737200-135743000	Enhancers	Rectal Smooth Muscle	rectum
21	chr3:135737400-135742200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:135737400-135747200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:135737600-135740000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:135737600-135741000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:135737800-135739800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:135737800-135740000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:135738000-135740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:135738000-135741400	Weak transcription	Right Atrium	heart
29	chr3:135738000-135741600	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:135738000-135741600	Weak transcription	Left Ventricle	heart
31	chr3:135738000-135741600	Weak transcription	Psoas Muscle	Psoas
32	chr3:135738000-135745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:135738000-135750000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:135738000-135758400	Weak transcription	Gastric	stomach
35	chr3:135738000-135761200	Weak transcription	Fetal Brain Male	brain
36	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:135738200-135740800	Weak transcription	NHEK	skin
38	chr3:135738200-135741000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:135738200-135741000	Weak transcription	HSMMtube	muscle
40	chr3:135738200-135741400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:135738200-135746600	Weak transcription	Fetal Stomach	stomach
42	chr3:135738200-135749600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:135738400-135741600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:135738400-135746400	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:135738400-135746800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:135738400-135763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:135738400-135763600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:135738600-135741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:135738600-135741600	Weak transcription	Right Ventricle	heart
50	chr3:135738600-135741800	Enhancers	Osteobl	bone

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