Variant report

Variant	rs890478
Chromosome Location	chr2:64540427-64540428
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64369964..64372694-chr2:64539391..64541388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225889	Chromatin interaction
ENSG00000197329	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10187442	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1030407	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030409	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1030410	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125996	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673882	0.86[ASN][1000 genomes]
rs11682772	0.84[ASN][1000 genomes]
rs11683866	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs11883600	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365474	0.81[ASN][1000 genomes]
rs1365475	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1426698	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs1426699	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1426701	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1426702	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1426712	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1974976	0.85[ASN][1000 genomes]
rs2059630	0.82[CEU][hapmap]
rs2263647	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278184	0.86[ASN][1000 genomes]
rs2555423	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555448	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4485554	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4597511	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546064	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546065	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66506765	0.82[ASN][1000 genomes]
rs6714101	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724171	0.82[ASN][1000 genomes]
rs6737527	0.82[ASN][1000 genomes]
rs6740438	0.82[ASN][1000 genomes]
rs6748843	0.83[ASN][1000 genomes]
rs6758664	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561343	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7565077	0.83[ASN][1000 genomes]
rs7585084	0.86[ASN][1000 genomes]
rs7601758	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7601803	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919122	0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs919123	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919124	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919126	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs919127	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930020	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64537600-64540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:64537800-64540800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:64537800-64540800	Enhancers	Fetal Muscle Leg	muscle
4	chr2:64537800-64540800	Enhancers	Fetal Stomach	stomach
5	chr2:64538000-64540600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:64538000-64540600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:64538200-64540600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:64538200-64540800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:64538200-64543800	Enhancers	Fetal Brain Male	brain
10	chr2:64538400-64540800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:64538400-64540800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:64538600-64540600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:64538600-64540800	Enhancers	Fetal Lung	lung
14	chr2:64538600-64540800	Enhancers	Left Ventricle	heart
15	chr2:64538800-64540800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:64538800-64540800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:64538800-64540800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:64538800-64540800	Enhancers	Colon Smooth Muscle	Colon
19	chr2:64538800-64540800	Enhancers	Fetal Muscle Trunk	muscle
20	chr2:64539200-64540800	Enhancers	Psoas Muscle	Psoas
21	chr2:64539200-64540800	Enhancers	Right Ventricle	heart
22	chr2:64539400-64540600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr2:64539600-64540800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:64539600-64540800	Enhancers	Liver	Liver
25	chr2:64539600-64540800	Enhancers	HSMMtube	muscle
26	chr2:64539800-64540800	Enhancers	Brain Germinal Matrix	brain
27	chr2:64539800-64543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:64539800-64549600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:64540000-64540600	Weak transcription	Pancreas	Pancrea
30	chr2:64540000-64540600	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:64540000-64541000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
33	chr2:64540200-64540600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:64540200-64540600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:64540200-64540600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:64540200-64540600	Weak transcription	Fetal Thymus	thymus
37	chr2:64540200-64540600	Enhancers	NHEK	skin
38	chr2:64540200-64540800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:64540200-64540800	Enhancers	Aorta	Aorta
40	chr2:64540200-64540800	Enhancers	Right Atrium	heart
41	chr2:64540200-64540800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:64540200-64540800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:64540200-64540800	Bivalent Enhancer	Osteobl	bone
44	chr2:64540200-64541000	Enhancers	Adipose Nuclei	Adipose
45	chr2:64540200-64542600	Weak transcription	Esophagus	oesophagus
46	chr2:64540200-64543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:64540200-64543600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:64540400-64540600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:64540400-64540800	Enhancers	Fetal Kidney	kidney

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