Variant report

Variant	rs1540909
Chromosome Location	chr6:35488853-35488854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35487540..35490871-chr6:35654917..35657662,3	MCF-7	breast:
2	chr6:35463713..35467638-chr6:35488845..35491546,5	K562	blood:
3	chr6:35464547..35467801-chr6:35485995..35490662,5	MCF-7	breast:
4	chr6:35462380..35467433-chr6:35484911..35489402,9	MCF-7	breast:
5	chr6:35477055..35480023-chr6:35485694..35489430,3	K562	blood:

Variant related genes	Relation type
ENSG00000007866	Chromatin interaction
ENSG00000112041	Chromatin interaction
ENSG00000096060	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2050162	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2064318	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2395630	0.84[EUR][1000 genomes]
rs2894402	0.90[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3807049	0.92[YRI][hapmap]
rs3997734	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4634451	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711420	0.86[ASN][1000 genomes]
rs4713879	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713882	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57630882	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457830	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6923949	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935833	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935976	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749522	0.80[EUR][1000 genomes]
rs7752728	1.00[GIH][hapmap]
rs7764472	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296155	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380516	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470048	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
2	nsv462909	chr6:35457396-35502202	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
3	nsv602912	chr6:35457396-35502202	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv2761067	chr6:35471246-35573245	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1022435	chr6:35476562-35556141	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1034786	chr6:35476562-35564799	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1031987	chr6:35476562-35579375	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1028302	chr6:35480914-35542591	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv538197	chr6:35480914-35542591	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1024680	chr6:35480914-35555596	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv538198	chr6:35480914-35555596	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv1032973	chr6:35481880-35564799	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35480200-35490800	Weak transcription	Right Atrium	heart
2	chr6:35480600-35490600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:35480800-35490200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:35482400-35489000	Enhancers	Placenta	Placenta
5	chr6:35484600-35490400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:35484800-35489200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:35487400-35489600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:35487600-35490400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:35487600-35490400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:35487600-35490600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:35487800-35489600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:35487800-35490200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:35487800-35490200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:35487800-35490400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:35487800-35490400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:35488000-35490000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:35488000-35490200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:35488000-35490200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:35488000-35490400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:35488000-35490400	Weak transcription	HMEC	breast
21	chr6:35488600-35490000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:35488800-35489000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:35488800-35489400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:35488800-35489400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr6:35488800-35490000	Bivalent Enhancer	HepG2	liver

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