Variant report

Variant	rs9370539
Chromosome Location	chr6:56454381-56454382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1014309	0.81[EUR][1000 genomes]
rs1014310	0.81[EUR][1000 genomes]
rs10456736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10484858	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11751914	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11969402	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12195236	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12200301	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12201550	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13194995	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13209548	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1474853	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16888055	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1884284	0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs1884285	0.85[CEU][hapmap];0.94[JPT][hapmap]
rs1884286	0.85[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs2024751	0.83[ASN][1000 genomes]
rs2144405	0.81[EUR][1000 genomes]
rs2230862	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36017808	0.81[EUR][1000 genomes]
rs4712135	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4712136	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712137	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4712138	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4715635	0.83[ASN][1000 genomes]
rs6459166	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6919941	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921099	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926648	0.81[EUR][1000 genomes]
rs6929091	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6931836	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7747060	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7759479	0.86[YRI][hapmap]
rs7760503	0.86[YRI][hapmap]
rs7772239	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349830	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9349831	0.88[ASN][1000 genomes]
rs9349832	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9349834	0.90[AMR][1000 genomes]
rs9349835	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349836	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357923	0.85[CEU][hapmap];0.93[JPT][hapmap]
rs9357927	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9367689	0.81[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap]
rs9367690	0.92[JPT][hapmap]
rs9370538	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370540	0.96[ASN][1000 genomes]
rs9370541	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370542	0.94[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370543	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370544	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9382650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382652	0.91[ASN][1000 genomes]
rs9382653	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9382654	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9382655	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382656	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382658	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382659	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9396222	0.91[ASN][1000 genomes]
rs9396224	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396225	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396228	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9475722	0.85[AFR][1000 genomes]
rs9475723	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9475724	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9689355	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9370539	BEND6	cis	cerebellum	SCAN

Chromatin state (count:96 , 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	chr6:56417800-56455400	Weak transcription	Gastric	stomach
7	chr6:56420400-56457400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:56420600-56455400	Weak transcription	Aorta	Aorta
9	chr6:56423800-56456200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:56426400-56455600	Weak transcription	Placenta	Placenta
11	chr6:56431200-56455400	Weak transcription	Ovary	ovary
12	chr6:56431400-56455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:56431400-56455400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:56431400-56455400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:56431400-56456800	Weak transcription	Right Ventricle	heart
16	chr6:56431600-56455400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
18	chr6:56435600-56458000	Weak transcription	Fetal Brain Female	brain
19	chr6:56436400-56464800	Weak transcription	Fetal Brain Male	brain
20	chr6:56438200-56455400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:56438200-56457800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:56438800-56456000	Weak transcription	Fetal Heart	heart
23	chr6:56438800-56458400	Weak transcription	HepG2	liver
24	chr6:56440800-56465800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
26	chr6:56441400-56455400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:56441600-56455400	Weak transcription	Brain Angular Gyrus	brain
28	chr6:56441600-56455400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:56441600-56465600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:56441800-56455400	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:56441800-56455400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:56444000-56455400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:56444400-56454800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:56444400-56455400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:56444600-56455400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:56444800-56455200	Weak transcription	NHEK	skin
37	chr6:56445200-56455400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr6:56445800-56455400	Weak transcription	Fetal Intestine Small	intestine
39	chr6:56446800-56455400	Weak transcription	Fetal Stomach	stomach
40	chr6:56447000-56455000	Weak transcription	NHLF	lung
41	chr6:56447400-56455400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:56452600-56457400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:56452800-56454400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:56452800-56454400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:56452800-56454600	ZNF genes & repeats	GM12878-XiMat	blood
48	chr6:56452800-56457600	Strong transcription	NHDF-Ad	bronchial
49	chr6:56452800-56458800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:56452800-56459800	Strong transcription	Fetal Lung	lung

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