Variant report

Variant	rs7673679
Chromosome Location	chr4:53419775-53419776
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10000311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10001370	0.84[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10010306	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10020568	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021143	0.90[ASN][1000 genomes]
rs10023867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10028085	0.86[ASN][1000 genomes]
rs10028755	1.00[ASN][1000 genomes]
rs10029145	0.90[ASN][1000 genomes]
rs10031386	0.90[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10033218	0.90[ASN][1000 genomes]
rs10471216	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28376189	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379922	0.86[ASN][1000 genomes]
rs28380682	0.90[ASN][1000 genomes]
rs28402205	0.90[ASN][1000 genomes]
rs28411005	0.90[ASN][1000 genomes]
rs28412170	0.90[ASN][1000 genomes]
rs28430452	0.90[ASN][1000 genomes]
rs28451750	0.90[ASN][1000 genomes]
rs28475600	0.90[ASN][1000 genomes]
rs28482298	0.90[ASN][1000 genomes]
rs28503210	0.90[ASN][1000 genomes]
rs28565016	0.90[ASN][1000 genomes]
rs28588481	0.84[ASN][1000 genomes]
rs28590396	0.90[ASN][1000 genomes]
rs28619184	0.90[ASN][1000 genomes]
rs28644292	0.90[ASN][1000 genomes]
rs28654693	0.90[ASN][1000 genomes]
rs28660550	0.90[ASN][1000 genomes]
rs28660571	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28672279	0.90[ASN][1000 genomes]
rs28694544	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28721897	0.90[ASN][1000 genomes]
rs28722174	0.90[ASN][1000 genomes]
rs28784684	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28825181	0.86[ASN][1000 genomes]
rs28825412	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28849759	0.90[ASN][1000 genomes]
rs28852068	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6830833	0.90[ASN][1000 genomes]
rs9990686	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9997863	1.00[AMR][1000 genomes];0.90[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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv879012	chr4:52976937-53421172	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999397	chr4:53157525-53448384	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv482581	chr4:53310749-53480710	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS 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
5	nsv1009480	chr4:53338708-53436560	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537092	chr4:53338708-53436560	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53416200-53420600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:53416600-53421000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr4:53416600-53421000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:53416600-53421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:53416800-53420200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:53416800-53420200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:53416800-53420400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:53416800-53420600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:53416800-53420600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:53416800-53420800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:53416800-53420800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:53417000-53420400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:53417000-53420400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:53417200-53420800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:53417200-53421200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:53417800-53427000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:53418000-53420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:53418200-53420400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:53419000-53420400	Weak transcription	Fetal Heart	heart
20	chr4:53419400-53420800	Weak transcription	HMEC	breast
21	chr4:53419400-53426600	Weak transcription	NHEK	skin
22	chr4:53419400-53426800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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