Variant report

Variant	rs715402
Chromosome Location	chr12:40731214-40731215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40730810..40731494-chr12:40768592..40769125,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1035812	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1035813	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10732751	0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10748040	0.94[JPT][hapmap]
rs10784518	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784536	0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs12306060	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1365763	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1365764	0.84[ASN][1000 genomes]
rs1365765	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1365766	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1388596	0.86[CHB][hapmap]
rs1427259	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs1427261	0.88[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs1427263	0.94[YRI][hapmap]
rs1427267	0.94[YRI][hapmap]
rs1427271	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1427272	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1427273	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1465527	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491939	0.81[CHB][hapmap]
rs1549562	0.82[EUR][1000 genomes]
rs17461964	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17484286	0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1816207	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs1822606	0.82[EUR][1000 genomes]
rs1834745	0.98[EUR][1000 genomes]
rs1834746	0.84[EUR][1000 genomes]
rs2069228	0.94[YRI][hapmap]
rs2081702	0.98[EUR][1000 genomes]
rs2162472	0.89[JPT][hapmap]
rs2404836	0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs2896975	0.94[YRI][hapmap]
rs2896978	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs3789330	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs3861083	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs3943893	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4099579	0.90[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs4465428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4473003	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767971	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767972	0.83[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4768231	0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768232	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768233	0.82[CHB][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768234	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768235	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768238	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5017705	0.89[JPT][hapmap]
rs6581723	0.88[JPT][hapmap]
rs7131694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7134572	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136122	0.88[JPT][hapmap]
rs7137437	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7137665	0.93[YRI][hapmap]
rs721709	0.94[YRI][hapmap]
rs7294952	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7294958	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7296657	0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302503	0.94[YRI][hapmap]
rs7305344	0.94[YRI][hapmap]
rs7306545	0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs7306684	0.80[EUR][1000 genomes]
rs7307310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308626	0.94[JPT][hapmap]
rs7311247	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7312497	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313525	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313895	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7314455	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7314863	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7954061	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7955042	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7956787	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7956898	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7957057	0.83[YRI][hapmap]
rs7957151	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7962116	0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs7962370	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7963086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963697	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7963987	0.94[JPT][hapmap]
rs7966143	0.82[EUR][1000 genomes]
rs7971919	0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs7976724	0.94[JPT][hapmap]
rs890575	0.94[JPT][hapmap]
rs919175	0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs963243	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
2	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:40674400-40760400	Weak transcription	Lung	lung
4	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
7	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
8	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
10	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:40721000-40734000	Weak transcription	Esophagus	oesophagus
12	chr12:40722400-40736200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:40722800-40755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:40724000-40731600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:40724200-40731400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:40724600-40745400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:40724800-40751000	Weak transcription	Brain Anterior Caudate	brain
18	chr12:40725000-40736200	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:40725000-40739200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr12:40725200-40732200	Strong transcription	Liver	Liver
21	chr12:40725200-40733200	Strong transcription	Primary B cells from cord blood	blood
22	chr12:40725200-40761200	Weak transcription	Psoas Muscle	Psoas
23	chr12:40726000-40734800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:40726200-40734600	Weak transcription	HMEC	breast
25	chr12:40726200-40766600	Weak transcription	A549	lung
26	chr12:40726200-40767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:40727400-40731600	Weak transcription	Right Ventricle	heart
28	chr12:40728600-40732000	Strong transcription	Adipose Nuclei	Adipose
29	chr12:40729600-40731600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:40729600-40731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:40729800-40756000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:40730000-40745800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:40730000-40747000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:40730000-40760000	Weak transcription	Spleen	Spleen
35	chr12:40730200-40731800	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:40730200-40732000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:40730200-40734000	Weak transcription	Ovary	ovary
38	chr12:40730400-40732000	Enhancers	Rectal Smooth Muscle	rectum
39	chr12:40730400-40734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:40730400-40745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:40730600-40734000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:40730600-40734600	Weak transcription	NHEK	skin
43	chr12:40730800-40731400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:40731200-40732400	Weak transcription	Fetal Heart	heart
45	chr12:40731200-40733200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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