Variant report

Variant	rs9464407
Chromosome Location	chr6:56779570-56779571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56777418..56779642-chr6:56786166..56787815,2	MCF-7	breast:
2	chr6:56777926..56779935-chr6:56789816..56792167,2	K562	blood:
3	chr6:56773281..56775523-chr6:56776609..56780879,5	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1007417	0.80[MEX][hapmap]
rs10498814	0.82[JPT][hapmap]
rs11962430	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11963350	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451705	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451706	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1562908	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs1599280	0.82[TSI][hapmap]
rs16888222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685218	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17685235	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903330	0.81[TSI][hapmap]
rs1903331	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2122958	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2397227	0.80[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs35301163	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818840	0.85[EUR][1000 genomes]
rs35942895	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58604217	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58721182	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59797084	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61273855	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411410	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62411427	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62411428	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411429	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459174	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925107	0.82[JPT][hapmap]
rs6941401	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720885	0.80[MEX][hapmap]
rs746010	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296856	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370552	0.80[CEU][hapmap]
rs9382669	0.86[MEX][hapmap]
rs9382670	0.86[MEX][hapmap]
rs9396246	0.86[MEX][hapmap]
rs9396250	0.82[JPT][hapmap];0.86[MEX][hapmap]
rs9464405	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475744	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475758	0.86[MEX][hapmap]
rs9475760	0.86[MEX][hapmap]

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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9464407	BEND6	cis	lymphoblastoid	seeQTL
rs9464407	BEND6	cis	Esophagus Muscularis	GTEx
rs9464407	DST	cis	cerebellum	SCAN
rs9464407	BEND6	cis	cerebellum	SCAN
rs9464407	BEND6	cis	Artery Tibial	GTEx
rs9464407	BEND6	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56774000-56779600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:56775800-56779600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:56775800-56780600	Enhancers	NHLF	lung
4	chr6:56775800-56781200	Enhancers	Osteobl	bone
5	chr6:56776600-56781200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:56777000-56779600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:56777000-56780400	Enhancers	HSMMtube	muscle
8	chr6:56777000-56781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:56777400-56781400	Enhancers	K562	blood
10	chr6:56777400-56781800	Weak transcription	HMEC	breast
11	chr6:56777600-56779800	Enhancers	Fetal Brain Female	brain
12	chr6:56777600-56792600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:56777600-56792600	Weak transcription	NH-A	brain
14	chr6:56777800-56779600	Weak transcription	GM12878-XiMat	blood
15	chr6:56777800-56780800	Enhancers	NHDF-Ad	bronchial
16	chr6:56777800-56782200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:56778000-56779600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:56778000-56781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:56778000-56782200	Enhancers	Fetal Brain Male	brain
20	chr6:56778200-56780800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:56778200-56781200	Enhancers	Brain Anterior Caudate	brain
22	chr6:56778400-56780400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:56778400-56781000	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:56778400-56792800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:56778800-56782000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:56779000-56779600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:56779000-56780400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:56779000-56780400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:56779000-56781000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:56779200-56779800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:56779200-56779800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:56779200-56779800	Enhancers	Placenta	Placenta
33	chr6:56779200-56779800	Enhancers	Fetal Thymus	thymus
34	chr6:56779200-56780600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:56779200-56780600	Enhancers	Brain Angular Gyrus	brain
36	chr6:56779400-56779600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr6:56779400-56779800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:56779400-56779800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:56779400-56780200	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:56779400-56780200	Enhancers	Fetal Heart	heart
41	chr6:56779400-56780400	Enhancers	Brain Substantia Nigra	brain

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