Variant report

Variant	rs746010
Chromosome Location	chr6:56800338-56800339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56799165..56801512-chr6:56813694..56816410,2	K562	blood:
2	chr6:56799400..56801740-chr6:56804250..56805836,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1007417	0.80[MEX][hapmap]
rs11962430	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11963350	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451705	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451706	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562908	0.86[MEX][hapmap]
rs1599280	0.82[TSI][hapmap]
rs16888222	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17685218	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17685235	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903330	0.81[TSI][hapmap]
rs1903331	0.94[EUR][1000 genomes]
rs2122958	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2397227	0.80[CEU][hapmap];0.84[CHB][hapmap];0.86[MEX][hapmap]
rs35301163	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35818840	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35942895	0.91[EUR][1000 genomes]
rs58604217	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58721182	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59797084	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61273855	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411410	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411427	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62411428	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411429	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459174	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6925107	0.84[CHB][hapmap]
rs6941401	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720885	0.80[MEX][hapmap]
rs9296855	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296856	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370552	0.80[CEU][hapmap]
rs9382669	0.86[MEX][hapmap]
rs9382670	0.86[MEX][hapmap]
rs9396246	0.86[MEX][hapmap]
rs9396250	0.86[MEX][hapmap]
rs9464405	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9464407	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475744	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475758	0.86[MEX][hapmap]
rs9475760	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs746010	BEND6	cis	Artery Tibial	GTEx
rs746010	DST	cis	cerebellum	SCAN
rs746010	BEND6	cis	Esophagus Muscularis	GTEx
rs746010	BEND6	cis	parietal	SCAN
rs746010	BEND6	cis	cerebellum	SCAN
rs746010	BEND6	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56792800-56802400	Weak transcription	A549	lung
2	chr6:56793000-56802600	Weak transcription	HSMM	muscle
3	chr6:56793200-56802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:56793200-56803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56793200-56803000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:56793200-56803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:56793200-56803200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:56796200-56803800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:56796800-56803800	Weak transcription	HSMMtube	muscle
10	chr6:56797600-56801600	Weak transcription	NHLF	lung
11	chr6:56798200-56801400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:56798600-56801800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:56798800-56801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:56798800-56803400	Weak transcription	K562	blood
15	chr6:56799200-56800400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:56799200-56801200	Weak transcription	GM12878-XiMat	blood
17	chr6:56799200-56802400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:56799200-56802400	Weak transcription	Hela-S3	cervix
19	chr6:56799400-56801400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:56799600-56800600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:56799800-56800400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:56799800-56800400	Enhancers	NH-A	brain
23	chr6:56799800-56800400	Enhancers	Osteobl	bone
24	chr6:56799800-56801600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:56800000-56801000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:56800200-56800400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:56800200-56801000	Weak transcription	NHDF-Ad	bronchial
28	chr6:56800200-56801600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:56800200-56802400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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