Variant report

Variant	rs335314
Chromosome Location	chr4:62386117-62386118
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	chr4:62340392..62342899-chr4:62384568..62386458,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11722703	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11725619	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11734047	1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11734084	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs186750	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1908438	0.87[ASW][hapmap];0.91[CHD][hapmap];1.00[YRI][hapmap]
rs2100593	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28716290	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs335299	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs335300	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs335306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs335307	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs335308	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs335310	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335311	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335313	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335316	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335318	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335319	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335321	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs335323	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4860095	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9992329	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9994628	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9994639	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2753138	chr4:62271444-62442507	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1005770	chr4:62344379-62398798	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv537109	chr4:62344379-62398798	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62378000-62386400	Weak transcription	Stomach Mucosa	stomach
2	chr4:62381000-62386400	Weak transcription	Brain Anterior Caudate	brain
3	chr4:62381400-62386600	Weak transcription	HMEC	breast
4	chr4:62381800-62386200	Weak transcription	NHEK	skin
5	chr4:62383200-62397800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:62383400-62386800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:62383400-62387200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:62383400-62387400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:62383400-62388600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:62383400-62388600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:62384400-62386800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:62384600-62386600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:62384600-62397800	Weak transcription	Brain Angular Gyrus	brain
14	chr4:62385000-62387400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:62385200-62386800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:62385200-62387200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr4:62385200-62387400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr4:62385600-62386200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:62385600-62386200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:62385600-62386800	Enhancers	Fetal Lung	lung
21	chr4:62385600-62387000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr4:62385600-62387600	Enhancers	NH-A	brain
23	chr4:62385800-62386400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:62385800-62386800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:62385800-62387200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr4:62385800-62388200	Enhancers	Fetal Heart	heart
27	chr4:62386000-62386200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:62386000-62386200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:62386000-62386400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:62386000-62386600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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