Variant report

Variant	rs538542
Chromosome Location	chr4:75054747-75054748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:75054682..75055658-chr4:75177289..75178153,3	MCF-7	breast:
2	chr4:75054721..75055635-chr4:75094051..75095124,3	K562	blood:
3	chr4:75054669..75056475-chr4:75229401..75230994,2	K562	blood:
4	chr4:75054653..75055732-chr4:75177181..75178135,3	K562	blood:
5	chr4:75051671..75055178-chr4:75229398..75232382,3	K562	blood:
6	chr4:75052779..75055705-chr4:75168128..75170187,2	MCF-7	breast:
7	chr4:75049836..75051355-chr4:75053800..75056077,2	K562	blood:

Variant related genes	Relation type
ENSG00000124882	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10026869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028397	1.00[JPT][hapmap]
rs10938111	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12163831	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12646785	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1265346	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13116686	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13136363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440407	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850531	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16850541	1.00[EUR][1000 genomes]
rs2289443	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs28823933	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs533352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535753	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537061	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538775	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs542458	0.84[EUR][1000 genomes]
rs547975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551906	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs564793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446975	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446976	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6824352	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs977597	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs977598	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75024800-75056600	Weak transcription	Pancreas	Pancrea
2	chr4:75024800-75080600	Weak transcription	Left Ventricle	heart
3	chr4:75025400-75067600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:75025400-75073600	Weak transcription	Right Ventricle	heart
5	chr4:75025600-75067600	Weak transcription	Thymus	Thymus
6	chr4:75028200-75067600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:75028800-75072800	Weak transcription	Liver	Liver
8	chr4:75030800-75055200	Weak transcription	NHEK	skin
9	chr4:75030800-75055800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:75034200-75071800	Weak transcription	HMEC	breast
11	chr4:75041200-75067000	Weak transcription	Primary T cells from cord blood	blood
12	chr4:75042600-75067400	Weak transcription	Fetal Thymus	thymus
13	chr4:75048400-75058800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:75048600-75060800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:75048600-75066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:75049400-75071400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:75050200-75065400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:75053200-75073400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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