Variant report

Variant	rs9475744
Chromosome Location	chr6:56761430-56761431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11962430	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11963350	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451705	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451706	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16888222	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685218	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17685235	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903331	0.85[EUR][1000 genomes]
rs35301163	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35942895	0.90[EUR][1000 genomes]
rs58604217	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58721182	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59797084	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61273855	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411410	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62411427	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62411428	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411429	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459174	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941401	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746010	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296855	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296856	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464405	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464407	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
10	nsv436516	chr6:56754861-56761823	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3330326	chr6:56757293-56762291	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	esv3523169	chr6:56757317-56762458	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
13	esv2555940	chr6:56757653-56761492	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
14	esv1002581	chr6:56758291-56767820	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9475744	BEND6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56749200-56769600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:56752400-56767000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:56753600-56769600	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:56755200-56762800	Weak transcription	Brain Anterior Caudate	brain
5	chr6:56756000-56762400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:56756000-56767000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:56756000-56767400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:56756000-56769600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:56756000-56769600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:56756000-56770000	Weak transcription	Brain Substantia Nigra	brain
11	chr6:56756200-56762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:56756200-56762400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:56756200-56764000	Weak transcription	NH-A	brain
14	chr6:56756200-56767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:56756200-56768400	Weak transcription	HMEC	breast
16	chr6:56756200-56768600	Weak transcription	HUVEC	blood vessel
17	chr6:56756200-56768800	Weak transcription	NHEK	skin
18	chr6:56756600-56767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:56756600-56775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:56756800-56762200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:56756800-56762400	Weak transcription	HSMM	muscle
22	chr6:56756800-56763800	Weak transcription	HSMMtube	muscle
23	chr6:56756800-56771600	Weak transcription	K562	blood
24	chr6:56757000-56762200	Weak transcription	NHLF	lung
25	chr6:56757000-56762600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:56757000-56762600	Weak transcription	Osteobl	bone
27	chr6:56757000-56763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:56757200-56763600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:56757200-56767400	Weak transcription	GM12878-XiMat	blood
30	chr6:56757400-56762200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:56757400-56762200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:56757600-56762400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:56757600-56762400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:56757600-56762400	Weak transcription	NHDF-Ad	bronchial
35	chr6:56759600-56767000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:56761000-56763400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:56761000-56763600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:56761000-56764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:56761000-56767400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:56761200-56762800	Weak transcription	Ovary	ovary
41	chr6:56761400-56763600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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