Variant report

Variant	rs9472541
Chromosome Location	chr6:45622748-45622749
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45387795..45389727-chr6:45621998..45623537,2	MCF-7	breast:
2	chr6:45615231..45620456-chr6:45620774..45624802,6	MCF-7	breast:
3	chr6:45620998..45623947-chr6:45624058..45626263,2	K562	blood:
4	chr6:45389165..45392210-chr6:45621811..45625140,4	MCF-7	breast:
5	chr6:45611643..45613817-chr6:45619919..45622769,2	K562	blood:

Variant related genes	Relation type
ENSG00000124813	Chromatin interaction
ENSG00000271857	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12175323	0.92[ASN][1000 genomes]
rs12661654	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12663985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12665728	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1388242	0.90[JPT][hapmap]
rs1388244	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1491139	0.91[EUR][1000 genomes]
rs1491144	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1491145	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1994682	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035791	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2396505	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs321321	0.82[CEU][hapmap]
rs321324	0.95[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs321325	0.94[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs4326224	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4714864	0.90[EUR][1000 genomes]
rs6458457	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458458	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7761790	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7762915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7769966	0.82[ASN][1000 genomes]
rs7774097	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9349322	0.89[ASN][1000 genomes]
rs9349324	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9357489	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9369569	0.80[ASN][1000 genomes]
rs9369572	0.92[EUR][1000 genomes]
rs9395110	0.81[ASN][1000 genomes]
rs9395111	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9472547	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9472548	0.92[ASN][1000 genomes]
rs9472552	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9472557	0.94[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45612400-45623600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:45615600-45626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:45617400-45627400	Enhancers	NHDF-Ad	bronchial
4	chr6:45617800-45624200	Enhancers	NHEK	skin
5	chr6:45617800-45627200	Enhancers	NHLF	lung
6	chr6:45618200-45627200	Weak transcription	Gastric	stomach
7	chr6:45618800-45623800	Enhancers	Osteobl	bone
8	chr6:45618800-45627200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:45619000-45623200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:45619000-45623800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:45619000-45624400	Enhancers	HUVEC	blood vessel
12	chr6:45619400-45623800	Enhancers	NH-A	brain
13	chr6:45620400-45626600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:45620600-45624000	Enhancers	HMEC	breast
15	chr6:45620800-45625800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:45620800-45626400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:45621000-45623800	Enhancers	Hela-S3	cervix
18	chr6:45621000-45625800	Weak transcription	Fetal Brain Male	brain
19	chr6:45621000-45626000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:45621400-45623800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr6:45621400-45625400	Weak transcription	Dnd41	blood
22	chr6:45621400-45626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:45621600-45624600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:45622200-45623200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:45622200-45624000	Enhancers	A549	lung
26	chr6:45622200-45624400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:45622200-45624400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:45622200-45625000	Enhancers	HSMMtube	muscle
29	chr6:45622400-45623800	Enhancers	HSMM	muscle
30	chr6:45622400-45624200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:45622600-45626000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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