Variant report

Variant	rs28449384
Chromosome Location	chr3:135693191-135693192
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135683614..135686835-chr3:135692106..135694532,3	MCF-7	breast:
2	chr3:135634384..135636473-chr3:135692724..135694710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10048942	1.00[ASN][1000 genomes]
rs10049233	1.00[ASN][1000 genomes]
rs10935175	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072596	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13082684	1.00[ASN][1000 genomes]
rs13097946	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13098245	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13322891	0.92[ASN][1000 genomes]
rs13325914	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1356664	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1401545	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1403766	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403767	0.92[ASN][1000 genomes]
rs1403770	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523595	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523596	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523597	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1568350	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17196987	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17197552	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17250445	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28570106	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28576629	1.00[ASN][1000 genomes]
rs28855968	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28875187	0.92[ASN][1000 genomes]
rs34311570	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34409306	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34522617	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34767379	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35257855	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35722356	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs36039354	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073308	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs55678980	0.92[ASN][1000 genomes]
rs56308637	0.92[ASN][1000 genomes]
rs67039922	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771224	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771997	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774289	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775778	1.00[ASN][1000 genomes]
rs6786769	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807058	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807242	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807565	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6810223	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71336046	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73222222	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7427833	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433567	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621331	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621396	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621425	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7628848	1.00[ASN][1000 genomes]
rs7641070	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643661	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs870812	0.92[ASN][1000 genomes]
rs908825	0.92[ASN][1000 genomes]
rs9289502	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289503	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9808979	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9812561	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814505	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9814557	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819440	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9820189	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826806	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9833699	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9834104	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9834624	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9836374	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9836758	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837355	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837855	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9842840	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9842864	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843725	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846137	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848322	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851361	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853577	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854494	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9862264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862743	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9862763	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862777	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864247	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9864514	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864775	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9868246	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9870581	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9872542	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9875328	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9875948	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9877082	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877722	0.92[ASN][1000 genomes]
rs9880721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135685600-135693800	Weak transcription	Gastric	stomach
2	chr3:135685800-135693800	Weak transcription	Lung	lung
3	chr3:135686600-135693400	Weak transcription	Right Ventricle	heart
4	chr3:135686600-135694400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:135687000-135693200	Weak transcription	Fetal Lung	lung
6	chr3:135687000-135693200	Weak transcription	Fetal Stomach	stomach
7	chr3:135687400-135693400	Weak transcription	Left Ventricle	heart
8	chr3:135687600-135694000	Enhancers	Colon Smooth Muscle	Colon
9	chr3:135687600-135700400	Weak transcription	Fetal Intestine Small	intestine
10	chr3:135688000-135694200	Enhancers	Brain Hippocampus Middle	brain
11	chr3:135688800-135694200	Enhancers	Brain Substantia Nigra	brain
12	chr3:135689400-135695200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:135690200-135694200	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:135690200-135701200	Weak transcription	NHEK	skin
15	chr3:135690200-135701400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:135690400-135694000	Weak transcription	HMEC	breast
17	chr3:135690400-135700800	Weak transcription	HSMM	muscle
18	chr3:135690600-135693200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:135690800-135693800	Weak transcription	NHDF-Ad	bronchial
20	chr3:135691000-135699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:135691200-135693400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr3:135691200-135699600	Weak transcription	Ovary	ovary
23	chr3:135691600-135694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:135691600-135694200	Enhancers	Brain Angular Gyrus	brain
25	chr3:135691600-135694400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:135691800-135693600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:135691800-135693800	Enhancers	Stomach Mucosa	stomach
28	chr3:135692000-135693400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:135692200-135693400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:135692200-135693400	Enhancers	Stomach Smooth Muscle	stomach
31	chr3:135692200-135694000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:135692200-135694200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:135692200-135694200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:135692200-135694200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:135692200-135694200	Enhancers	Psoas Muscle	Psoas
36	chr3:135692400-135694000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:135692400-135694400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:135692600-135693400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:135692600-135693400	Enhancers	NHLF	lung
40	chr3:135692600-135693600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:135692600-135693800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:135692600-135693800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:135692600-135694000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:135692600-135694000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:135692600-135694000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:135692600-135694200	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:135692600-135694200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:135692600-135694200	Enhancers	Fetal Heart	heart
49	chr3:135692800-135693400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:135692800-135693400	Enhancers	Fetal Kidney	kidney

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