Variant report

Variant	rs9396225
Chromosome Location	chr6:56455855-56455856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1014309	0.81[EUR][1000 genomes]
rs1014310	0.81[EUR][1000 genomes]
rs10456736	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10484858	0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11751914	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11969402	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12195236	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12200301	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12201550	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13194995	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13209548	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474853	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16888055	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1884284	0.82[CHD][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs1884285	0.94[JPT][hapmap]
rs1884286	0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs2024751	0.85[ASN][1000 genomes]
rs2144405	0.81[EUR][1000 genomes]
rs2230862	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36017808	0.81[EUR][1000 genomes]
rs4712135	0.90[EUR][1000 genomes]
rs4712136	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712137	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712138	0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715635	0.85[ASN][1000 genomes]
rs6459166	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6919941	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6921099	0.83[EUR][1000 genomes]
rs6926648	0.81[EUR][1000 genomes]
rs6929091	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6931836	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7747060	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7772239	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349830	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9349832	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349834	0.89[AMR][1000 genomes]
rs9349835	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349836	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357923	0.93[JPT][hapmap]
rs9357927	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9367689	0.88[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs9367690	0.92[JPT][hapmap]
rs9370538	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370539	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370540	0.86[ASN][1000 genomes]
rs9370541	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370542	0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370543	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370544	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9382650	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382652	0.80[ASN][1000 genomes]
rs9382653	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9382654	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9382655	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382656	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382658	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382659	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9396222	0.80[ASN][1000 genomes]
rs9396224	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396228	0.81[EUR][1000 genomes]
rs9475723	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9475724	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9689355	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9396225	BEND6	cis	cerebellum	SCAN
rs9396225	BMP5	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
4	chr6:56417200-56462000	Weak transcription	Lung	lung
5	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
6	chr6:56420400-56457400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:56423800-56456200	Weak transcription	Brain Substantia Nigra	brain
8	chr6:56431400-56456800	Weak transcription	Right Ventricle	heart
9	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
10	chr6:56435600-56458000	Weak transcription	Fetal Brain Female	brain
11	chr6:56436400-56464800	Weak transcription	Fetal Brain Male	brain
12	chr6:56438200-56457800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:56438800-56456000	Weak transcription	Fetal Heart	heart
14	chr6:56438800-56458400	Weak transcription	HepG2	liver
15	chr6:56440800-56465800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
17	chr6:56441600-56465600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:56452600-56457400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:56452800-56457600	Strong transcription	NHDF-Ad	bronchial
22	chr6:56452800-56458800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:56452800-56459800	Strong transcription	Fetal Lung	lung
24	chr6:56452800-56469200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:56452800-56470000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:56452800-56476000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:56452800-56489400	Strong transcription	Liver	Liver
28	chr6:56453000-56456400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:56453000-56457000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:56453000-56457000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:56453000-56457400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:56453000-56457400	Strong transcription	Left Ventricle	heart
33	chr6:56453000-56458400	Weak transcription	Fetal Kidney	kidney
34	chr6:56453000-56458600	Strong transcription	Osteobl	bone
35	chr6:56453000-56459600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:56453000-56460400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:56453000-56468800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:56453000-56469000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:56453000-56469000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:56453000-56469200	Strong transcription	Fetal Intestine Large	intestine
41	chr6:56453000-56469800	Strong transcription	NH-A	brain
42	chr6:56453000-56492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:56453000-56502200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr6:56453000-56506800	Strong transcription	HSMM	muscle
45	chr6:56453200-56470000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:56453400-56456000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:56453400-56456400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr6:56453400-56458600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:56453400-56469200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:56453400-56476200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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