Variant report

Variant	rs4699644
Chromosome Location	chr4:99457545-99457546
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	chr4:99457417..99457920-chr6:115486765..115487390,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10002696	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10006366	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10006430	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10018825	0.92[CEU][hapmap]
rs10021296	0.96[CEU][hapmap]
rs10025051	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097619	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13108940	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13123700	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13141997	0.88[CEU][hapmap]
rs13149070	0.96[CEU][hapmap]
rs1528547	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1534554	0.84[ASN][1000 genomes]
rs1534555	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs1573478	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1919210	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1919211	0.81[CEU][hapmap]
rs2037832	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866017	0.91[CEU][hapmap]
rs28886705	0.88[ASN][1000 genomes]
rs4447870	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699343	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699345	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4699348	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699349	0.92[CEU][hapmap]
rs4699639	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699640	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699646	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4699648	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6532742	0.92[CEU][hapmap]
rs6815038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823547	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6831643	0.92[CEU][hapmap]
rs6837359	0.96[CEU][hapmap]
rs6847124	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs71600251	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7672134	0.96[CEU][hapmap]
rs9760870	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99440400-99458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:99445200-99461800	Weak transcription	HMEC	breast
3	chr4:99445400-99465400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:99446000-99467400	Weak transcription	Fetal Stomach	stomach
5	chr4:99446800-99461600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:99448200-99461000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:99449400-99461200	Weak transcription	NHEK	skin
8	chr4:99449400-99464200	Weak transcription	Fetal Brain Female	brain
9	chr4:99449800-99467400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:99450200-99458400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:99450200-99467400	Weak transcription	Osteobl	bone
12	chr4:99450400-99461800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:99450400-99465200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:99450800-99458800	Weak transcription	NHLF	lung
15	chr4:99450800-99468000	Weak transcription	HSMM	muscle
16	chr4:99451600-99458800	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:99451800-99458200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:99457000-99458200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr4:99457000-99459600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:99457200-99457800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:99457200-99457800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:99457200-99458400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:99457200-99458400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:99457200-99458400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:99457400-99457600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr4:99457400-99457600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:99457400-99457600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:99457400-99457800	Enhancers	Ovary	ovary
29	chr4:99457400-99458200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:99457400-99458400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:99457400-99458400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr4:99457400-99458600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr4:99457400-99459000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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