Variant report

Variant	rs11962430
Chromosome Location	chr6:56774756-56774757
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56772967..56775962-chr6:56913388..56915663,2	K562	blood:
2	chr6:56770313..56772562-chr6:56773630..56775659,2	K562	blood:
3	chr6:56773281..56775523-chr6:56776609..56780879,5	K562	blood:
4	chr6:56773027..56775523-chr6:56776633..56778873,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10498814	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs11963350	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451705	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451706	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1562908	0.82[JPT][hapmap]
rs16888222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17685218	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17685235	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
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]
rs35301163	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.91[ASN][1000 genomes]
rs58721182	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59797084	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61273855	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411410	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62411427	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62411428	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411429	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6459174	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925107	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6941401	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746010	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370552	0.81[CEU][hapmap]
rs9396250	0.82[JPT][hapmap]
rs9464405	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9464407	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475744	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475752	0.80[AFR][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11962430	BEND6	cis	Artery Tibial	GTEx
rs11962430	BEND6	cis	Esophagus Muscularis	GTEx
rs11962430	BEND6	cis	lung	GTEx
rs11962430	BEND6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56756600-56775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56766000-56775800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56767600-56775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:56768000-56775600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:56768200-56775600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:56770000-56776800	Weak transcription	Placenta	Placenta
7	chr6:56770000-56779200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:56770200-56776200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:56771400-56775000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:56771600-56777600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:56772000-56775800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:56772000-56777400	Weak transcription	K562	blood
13	chr6:56772200-56775800	Weak transcription	NHLF	lung
14	chr6:56772800-56775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:56774000-56774800	Enhancers	NH-A	brain
16	chr6:56774000-56774800	Enhancers	Osteobl	bone
17	chr6:56774000-56775000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:56774000-56775200	Enhancers	HSMM	muscle
19	chr6:56774000-56776200	Enhancers	NHDF-Ad	bronchial
20	chr6:56774000-56779600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:56774200-56774800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:56774200-56774800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:56774200-56774800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:56774200-56774800	Enhancers	HSMMtube	muscle
25	chr6:56774200-56775000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:56774200-56776200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:56774400-56775000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:56774600-56775600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:56774600-56775600	Weak transcription	NHEK	skin
30	chr6:56774600-56775800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:56774600-56775800	Weak transcription	A549	lung
32	chr6:56774600-56776000	Weak transcription	HMEC	breast

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