Variant report

Variant	rs12638030
Chromosome Location	chr3:112985485-112985486
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	chr3:112980495..112983266-chr3:112984401..112987231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10511323	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11710894	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11717833	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11928342	0.90[JPT][hapmap];0.87[AMR][1000 genomes]
rs12485329	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492273	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494864	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12631733	0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16860758	0.94[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16860787	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875111	0.90[JPT][hapmap]
rs2036282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270781	0.81[JPT][hapmap]
rs34284771	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814398	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3846046	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856718	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856719	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856720	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682131	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682132	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682478	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682479	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682480	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4682481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682483	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73235136	0.81[ASN][1000 genomes]
rs73235142	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73235143	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235147	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73235153	0.83[ASN][1000 genomes]
rs7641410	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs775222	0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
9	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:112976400-112988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:112979600-112985600	Enhancers	Fetal Brain Female	brain
13	chr3:112981000-112986600	Enhancers	Brain Substantia Nigra	brain
14	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
15	chr3:112981400-112987200	Weak transcription	Aorta	Aorta
16	chr3:112981400-112989800	Weak transcription	Gastric	stomach
17	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:112982000-112985600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:112982000-112985800	Weak transcription	Esophagus	oesophagus
20	chr3:112982000-112986200	Weak transcription	Ovary	ovary
21	chr3:112982000-112989800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:112982200-112986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:112982200-112987200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:112982200-112988800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:112982200-112989400	Weak transcription	Adipose Nuclei	Adipose
26	chr3:112982600-112989000	Weak transcription	NHEK	skin
27	chr3:112982800-112985800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:112982800-112993600	Weak transcription	HMEC	breast
29	chr3:112983000-112987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:112983000-112987400	Weak transcription	NHDF-Ad	bronchial
31	chr3:112983400-112986800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:112983600-112985800	Enhancers	Fetal Kidney	kidney
33	chr3:112983800-112995000	Weak transcription	Lung	lung
34	chr3:112984000-112986600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:112984000-112987000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
37	chr3:112984200-112986000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:112984200-112987000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:112984200-112987200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:112984200-112987200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:112984200-112987400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:112984200-112987800	Weak transcription	Pancreas	Pancrea
43	chr3:112984200-112989800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:112984200-112994400	Weak transcription	HSMM	muscle
46	chr3:112984400-112985800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:112984400-112987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:112984400-112987200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:112984600-112986000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr3:112984600-112988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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