Variant report

Variant	rs6532742
Chromosome Location	chr4:99462534-99462535
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	chr4:99460334..99463092-chr4:99464059..99466192,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10002696	0.92[CEU][hapmap]
rs10006366	0.92[CEU][hapmap]
rs10018825	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs10021296	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs10025051	0.92[CEU][hapmap]
rs11097621	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730384	0.94[JPT][hapmap]
rs13108940	0.92[CEU][hapmap]
rs13114571	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13132635	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13134231	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13141997	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13149070	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs1534555	0.92[CEU][hapmap]
rs1573478	0.88[CEU][hapmap]
rs17191936	0.81[CHB][hapmap]
rs17192060	0.83[CHB][hapmap]
rs1919211	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2037832	0.92[CEU][hapmap]
rs2866017	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs4699343	0.92[CEU][hapmap]
rs4699346	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699348	0.92[CEU][hapmap]
rs4699349	0.92[CEU][hapmap]
rs4699639	0.92[CEU][hapmap]
rs4699640	0.92[CEU][hapmap]
rs4699644	0.92[CEU][hapmap]
rs4699650	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699651	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699652	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532744	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532745	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532747	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532748	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6827510	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831464	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6837359	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs6846287	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6854339	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672134	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs7695093	0.83[CHB][hapmap]

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	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99445400-99465400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:99446000-99467400	Weak transcription	Fetal Stomach	stomach
3	chr4:99449400-99464200	Weak transcription	Fetal Brain Female	brain
4	chr4:99449800-99467400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:99450200-99467400	Weak transcription	Osteobl	bone
6	chr4:99450400-99465200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:99450800-99468000	Weak transcription	HSMM	muscle
8	chr4:99458200-99465400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:99458800-99464400	Enhancers	Ovary	ovary
10	chr4:99459000-99468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:99459200-99465000	Weak transcription	Fetal Brain Male	brain
12	chr4:99459200-99468000	Weak transcription	Esophagus	oesophagus
13	chr4:99459200-99479600	Weak transcription	Spleen	Spleen
14	chr4:99459600-99465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:99459600-99465400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:99459600-99465400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:99459600-99466000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:99459600-99467800	Weak transcription	NHLF	lung
19	chr4:99459800-99465400	Weak transcription	Brain Anterior Caudate	brain
20	chr4:99460200-99463400	Weak transcription	Fetal Heart	heart
21	chr4:99460600-99463400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:99461000-99467400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:99461200-99464200	Enhancers	NHEK	skin
24	chr4:99461200-99465400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:99461600-99462600	Enhancers	Brain Substantia Nigra	brain
26	chr4:99461600-99464000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:99461800-99463000	Enhancers	Brain Hippocampus Middle	brain
28	chr4:99461800-99463200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:99461800-99463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:99461800-99463600	Enhancers	HMEC	breast
31	chr4:99461800-99463800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:99462400-99465400	Weak transcription	Brain Angular Gyrus	brain

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