Variant report

Variant	rs9475724
Chromosome Location	chr6:56436335-56436336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1014309	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1014310	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10456736	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10484858	0.86[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]
rs10807515	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10949003	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11751914	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11969402	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12195236	0.81[EUR][1000 genomes]
rs12200301	0.88[EUR][1000 genomes]
rs12201550	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13197391	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13209548	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1474853	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1474854	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1884284	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1884285	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1884286	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2067543	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2144405	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2230862	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28759439	0.89[EUR][1000 genomes]
rs34049027	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34237663	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36017808	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712136	0.81[EUR][1000 genomes]
rs4712138	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs6459166	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6919941	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6920543	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6926648	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6929091	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6931836	0.88[EUR][1000 genomes]
rs7747060	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7772239	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9349829	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9349830	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9349832	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9349834	0.88[AMR][1000 genomes]
rs9349835	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9357923	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs9357924	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9367689	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9367690	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370538	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370539	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370541	0.81[EUR][1000 genomes]
rs9370542	0.89[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9370543	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9382645	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9382650	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382653	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs9382656	0.82[EUR][1000 genomes]
rs9382658	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9396221	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9396224	0.81[EUR][1000 genomes]
rs9396225	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9475719	0.84[EUR][1000 genomes]
rs9475721	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9475722	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9475723	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9689355	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9475724	BEND6	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
6	chr6:56417200-56462000	Weak transcription	Lung	lung
7	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
8	chr6:56417800-56454200	Weak transcription	Psoas Muscle	Psoas
9	chr6:56417800-56455400	Weak transcription	Gastric	stomach
10	chr6:56420400-56457400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:56420600-56437600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:56420600-56440400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:56420600-56454000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:56420600-56455400	Weak transcription	Aorta	Aorta
15	chr6:56420800-56438000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:56423800-56456200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:56426400-56444200	Weak transcription	HUVEC	blood vessel
18	chr6:56426400-56455600	Weak transcription	Placenta	Placenta
19	chr6:56427600-56440600	Weak transcription	Colonic Mucosa	Colon
20	chr6:56428200-56437000	Strong transcription	Liver	Liver
21	chr6:56429000-56440000	Weak transcription	Spleen	Spleen
22	chr6:56429000-56443800	Weak transcription	Stomach Mucosa	stomach
23	chr6:56429000-56444800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:56429200-56444400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:56429200-56447400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:56429400-56439200	Strong transcription	HSMM	muscle
27	chr6:56430400-56436800	Strong transcription	HSMMtube	muscle
28	chr6:56430800-56438800	Strong transcription	Osteobl	bone
29	chr6:56431200-56455400	Weak transcription	Ovary	ovary
30	chr6:56431400-56438200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:56431400-56440200	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:56431400-56454200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:56431400-56455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:56431400-56455400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:56431400-56455400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:56431400-56456800	Weak transcription	Right Ventricle	heart
37	chr6:56431600-56441800	Strong transcription	GM12878-XiMat	blood
38	chr6:56431600-56455400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:56431800-56437400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:56431800-56453000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:56432000-56437000	Weak transcription	Adipose Nuclei	Adipose
42	chr6:56432000-56440800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:56432400-56438400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:56432400-56438800	Strong transcription	NHDF-Ad	bronchial
45	chr6:56432600-56437000	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:56432600-56440200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:56432800-56437600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:56432800-56437600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:56432800-56438600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine

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