Variant report

Variant	rs9475752
Chromosome Location	chr6:56780741-56780742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56780041..56782514-chr6:56808634..56811006,2	K562	blood:
2	chr6:56779944..56782895-chr6:56786364..56788046,2	MCF-7	breast:
3	chr6:56773281..56775523-chr6:56776609..56780879,5	K562	blood:

Variant related genes	Relation type
ENSG00000200224	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11962430	0.80[AFR][1000 genomes]
rs11963379	1.00[ASN][1000 genomes]
rs13215865	0.81[EUR][1000 genomes]
rs13220510	0.99[EUR][1000 genomes]
rs1451707	0.94[EUR][1000 genomes]
rs1451708	0.94[EUR][1000 genomes]
rs1460561	0.98[EUR][1000 genomes]
rs1599280	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1599281	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17450853	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685143	0.98[EUR][1000 genomes]
rs17685185	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752412	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752435	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752459	0.98[EUR][1000 genomes]
rs1903330	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs34232358	0.81[EUR][1000 genomes]
rs34259328	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34714091	0.81[EUR][1000 genomes]
rs34733863	0.82[EUR][1000 genomes]
rs34752771	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812189	0.90[EUR][1000 genomes]
rs35202312	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35434542	0.89[EUR][1000 genomes]
rs35527216	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860642	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35961728	0.89[EUR][1000 genomes]
rs36112505	0.93[EUR][1000 genomes]
rs4490669	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786720	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56030203	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58338781	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59524770	1.00[ASN][1000 genomes]
rs60547490	1.00[ASN][1000 genomes]
rs61340009	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71550519	0.99[EUR][1000 genomes]
rs71564866	0.98[EUR][1000 genomes]
rs71564868	0.98[EUR][1000 genomes]
rs73459728	0.91[ASN][1000 genomes]
rs73459729	1.00[ASN][1000 genomes]
rs73459735	1.00[ASN][1000 genomes]
rs73463711	1.00[ASN][1000 genomes]
rs748996	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296855	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs9296856	0.80[AFR][1000 genomes]
rs9475745	1.00[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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 miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9475752	BEND6	cis	Artery Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56775800-56781200	Enhancers	Osteobl	bone
2	chr6:56776600-56781200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:56777000-56781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:56777400-56781400	Enhancers	K562	blood
5	chr6:56777400-56781800	Weak transcription	HMEC	breast
6	chr6:56777600-56792600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:56777600-56792600	Weak transcription	NH-A	brain
8	chr6:56777800-56780800	Enhancers	NHDF-Ad	bronchial
9	chr6:56777800-56782200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:56778000-56781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:56778000-56782200	Enhancers	Fetal Brain Male	brain
12	chr6:56778200-56780800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:56778200-56781200	Enhancers	Brain Anterior Caudate	brain
14	chr6:56778400-56781000	Enhancers	Brain Cingulate Gyrus	brain
15	chr6:56778400-56792800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56778800-56782000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:56779000-56781000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:56779600-56782000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:56779800-56780800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:56779800-56782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:56779800-56782800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:56780400-56781200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:56780400-56781200	Enhancers	Fetal Brain Female	brain
24	chr6:56780400-56781800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:56780600-56780800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr6:56780600-56781800	Weak transcription	GM12878-XiMat	blood
27	chr6:56780600-56792600	Weak transcription	NHLF	lung

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