Variant report

Variant	rs12640660
Chromosome Location	chr4:148689877-148689878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148649361..148653898-chr4:148687606..148694872,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10027921	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11099669	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1119887	0.89[JPT][hapmap]
rs11729081	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12502667	1.00[MEX][hapmap]
rs12645249	1.00[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12648074	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13134018	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1604785	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs17023770	0.94[TSI][hapmap]
rs17023844	0.89[JPT][hapmap]
rs2055551	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2118036	0.85[ASW][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap]
rs2134706	0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2164527	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4835456	0.84[CHB][hapmap]
rs62330668	0.86[AMR][1000 genomes]
rs6535556	0.90[JPT][hapmap];1.00[MEX][hapmap]
rs6535558	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6535559	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6535560	0.96[AFR][1000 genomes]
rs6535561	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6822971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6836509	1.00[MEX][hapmap]
rs6839987	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6840039	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6845560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7673234	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7673606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9332471	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs964170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880242	chr4:148659137-148727355	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148670200-148693200	Weak transcription	Esophagus	oesophagus
2	chr4:148678000-148693200	Weak transcription	Adipose Nuclei	Adipose
3	chr4:148679200-148693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:148679200-148693000	Weak transcription	Aorta	Aorta
5	chr4:148679200-148696400	Weak transcription	Lung	lung
6	chr4:148682200-148693000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:148682400-148692400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:148684200-148691800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:148684400-148693600	Weak transcription	Fetal Kidney	kidney
10	chr4:148685200-148692200	Weak transcription	Right Atrium	heart
11	chr4:148685600-148691200	Weak transcription	Psoas Muscle	Psoas
12	chr4:148686000-148693000	Weak transcription	Ovary	ovary
13	chr4:148687000-148692000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:148687200-148696400	Weak transcription	Right Ventricle	heart
15	chr4:148687400-148691800	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:148688600-148691400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:148688800-148690000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:148688800-148690200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:148688800-148690200	Enhancers	HSMM	muscle
20	chr4:148688800-148690400	Enhancers	GM12878-XiMat	blood
21	chr4:148688800-148690400	Enhancers	HMEC	breast
22	chr4:148688800-148690600	Enhancers	NH-A	brain
23	chr4:148688800-148690600	Enhancers	NHDF-Ad	bronchial
24	chr4:148688800-148691000	Enhancers	Osteobl	bone
25	chr4:148688800-148693400	Enhancers	HUVEC	blood vessel
26	chr4:148689000-148690000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:148689000-148690000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:148689000-148693200	Enhancers	NHEK	skin
29	chr4:148689200-148691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:148689400-148690400	Weak transcription	Fetal Heart	heart
31	chr4:148689400-148690400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:148689400-148691400	Weak transcription	Fetal Intestine Small	intestine
33	chr4:148689400-148691800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:148689400-148692000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:148689400-148692800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:148689400-148693000	Weak transcription	Fetal Intestine Large	intestine
37	chr4:148689400-148693000	Weak transcription	Pancreas	Pancrea
38	chr4:148689400-148693000	Weak transcription	Small Intestine	intestine
39	chr4:148689400-148698000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:148689600-148690600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:148689600-148690800	Weak transcription	A549	lung
42	chr4:148689600-148691200	Weak transcription	HSMMtube	muscle
43	chr4:148689600-148691600	Weak transcription	NHLF	lung
44	chr4:148689600-148692200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:148689600-148693000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:148689600-148693000	Weak transcription	Gastric	stomach
47	chr4:148689600-148693000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:148689600-148693200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:148689600-148693200	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:148689600-148693400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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