Variant report

Variant	rs9296855
Chromosome Location	chr6:56769980-56769981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56768468..56773680-chr6:56817098..56821672,5	MCF-7	breast:
2	chr6:56769451..56770050-chr6:56819340..56821302,7	MCF-7	breast:
3	chr6:56767586..56771762-chr6:56818503..56821591,4	K562	blood:
4	chr6:56769552..56770203-chr6:57189093..57189825,2	MCF-7	breast:
5	chr6:56766600..56772134-chr6:56817595..56821119,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10498814	0.82[JPT][hapmap]
rs11962430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11963350	0.93[AFR][1000 genomes];0.94[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];0.81[MEX][hapmap]
rs1599280	0.82[TSI][hapmap]
rs16888222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	0.87[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];0.81[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	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58604217	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58721182	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[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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925107	0.82[JPT][hapmap]
rs6941401	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746010	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7744240	0.81[MEX][hapmap]
rs9296856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370552	0.80[CEU][hapmap]
rs9382669	0.81[MEX][hapmap]
rs9382670	0.81[MEX][hapmap]
rs9396246	0.81[MEX][hapmap]
rs9396250	0.82[JPT][hapmap];0.81[MEX][hapmap]
rs9464405	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464407	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475744	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475752	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs9475758	0.81[MEX][hapmap]
rs9475760	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9296855	DST	cis	cerebellum	SCAN
rs9296855	BEND6	cis	Heart Left Ventricle	GTEx
rs9296855	BEND6	cis	lymphoblastoid	seeQTL
rs9296855	RAB23	cis	multi-tissue	Pritchard
rs9296855	BEND6	cis	Esophagus Muscularis	GTEx
rs9296855	BEND6	cis	lung	GTEx
rs9296855	BEND6	cis	parietal	SCAN
rs9296855	BEND6	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56756000-56770000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:56756600-56775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:56756800-56771600	Weak transcription	K562	blood
4	chr6:56763800-56774000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56764800-56771400	Weak transcription	NH-A	brain
6	chr6:56765000-56771600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:56765800-56770000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:56766000-56775800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:56767600-56770400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:56767600-56775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:56767800-56771200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:56768000-56775600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:56768200-56771200	Weak transcription	NHLF	lung
14	chr6:56768200-56771600	Weak transcription	HSMM	muscle
15	chr6:56768200-56771600	Weak transcription	HSMMtube	muscle
16	chr6:56768200-56771600	Weak transcription	Osteobl	bone
17	chr6:56768200-56774200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:56768200-56775600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:56768400-56770000	Enhancers	HMEC	breast
20	chr6:56768400-56770200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:56768800-56770200	Enhancers	NHDF-Ad	bronchial
22	chr6:56769200-56770000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:56769400-56770000	Active TSS	A549	lung
24	chr6:56769600-56770000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:56769600-56770000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:56769600-56770000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:56769600-56770000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:56769600-56770000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:56769600-56770000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:56769600-56770000	Enhancers	Brain Angular Gyrus	brain
31	chr6:56769600-56770000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:56769600-56770000	Enhancers	Placenta	Placenta
33	chr6:56769600-56770000	Enhancers	Ovary	ovary
34	chr6:56769600-56770000	Flanking Active TSS	Hela-S3	cervix
35	chr6:56769600-56770200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:56769600-56770200	Enhancers	NHEK	skin
37	chr6:56769800-56770000	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr6:56769800-56770000	Enhancers	GM12878-XiMat	blood
39	chr6:56769800-56770000	Enhancers	HepG2	liver
40	chr6:56769800-56770200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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