Variant report

Variant	rs2024751
Chromosome Location	chr6:56444168-56444169
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1014309	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1014310	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10484858	0.89[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10807515	0.81[EUR][1000 genomes]
rs11751914	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11969402	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12195236	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12200301	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194995	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13197391	0.81[EUR][1000 genomes]
rs13209548	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474854	0.80[EUR][1000 genomes]
rs16888055	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884284	0.81[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1884285	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1884286	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs2144405	0.82[EUR][1000 genomes]
rs34049027	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34237663	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36017808	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4712136	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712137	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4712138	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4715635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459166	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6919941	0.83[ASN][1000 genomes]
rs6921099	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926648	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6929091	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6931836	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71564846	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7747060	0.80[ASN][1000 genomes]
rs7772239	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9349829	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9349831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349832	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349835	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9349836	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357923	0.80[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs9357924	0.80[EUR][1000 genomes]
rs9357927	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367689	0.83[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9367690	0.81[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9370538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370539	0.83[ASN][1000 genomes]
rs9370540	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9370541	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370542	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370544	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382645	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9382650	0.83[ASN][1000 genomes]
rs9382652	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382653	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382654	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382655	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9382656	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382658	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382659	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9396221	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9396222	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9396224	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396225	0.85[ASN][1000 genomes]
rs9396228	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9475721	0.80[EUR][1000 genomes]
rs9475722	0.81[EUR][1000 genomes]
rs9475723	0.82[EUR][1000 genomes]
rs9689355	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[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
rs2024751	BEND6	cis	cerebellum	SCAN

Chromatin state (count:94 , 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	chr6:56417800-56454200	Weak transcription	Psoas Muscle	Psoas
7	chr6:56417800-56455400	Weak transcription	Gastric	stomach
8	chr6:56420400-56457400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr6:56420600-56454000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:56420600-56455400	Weak transcription	Aorta	Aorta
11	chr6:56423800-56456200	Weak transcription	Brain Substantia Nigra	brain
12	chr6:56426400-56444200	Weak transcription	HUVEC	blood vessel
13	chr6:56426400-56455600	Weak transcription	Placenta	Placenta
14	chr6:56429000-56444800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:56429200-56444400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:56429200-56447400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:56431200-56455400	Weak transcription	Ovary	ovary
18	chr6:56431400-56454200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:56431400-56455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:56431400-56455400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:56431400-56455400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:56431400-56456800	Weak transcription	Right Ventricle	heart
23	chr6:56431600-56455400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:56431800-56453000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
26	chr6:56433200-56444200	Strong transcription	NH-A	brain
27	chr6:56434200-56444200	Weak transcription	NHEK	skin
28	chr6:56435600-56458000	Weak transcription	Fetal Brain Female	brain
29	chr6:56435800-56453000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:56436000-56444400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:56436000-56444400	Weak transcription	Brain Germinal Matrix	brain
32	chr6:56436000-56453000	Weak transcription	A549	lung
33	chr6:56436400-56464800	Weak transcription	Fetal Brain Male	brain
34	chr6:56438000-56445800	Weak transcription	Fetal Kidney	kidney
35	chr6:56438000-56446200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:56438000-56454200	Weak transcription	HMEC	breast
37	chr6:56438200-56455400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:56438200-56457800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:56438600-56453000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:56438800-56456000	Weak transcription	Fetal Heart	heart
41	chr6:56438800-56458400	Weak transcription	HepG2	liver
42	chr6:56439800-56444200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:56439800-56444200	Strong transcription	HSMMtube	muscle
44	chr6:56439800-56446200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:56440200-56444800	Strong transcription	Liver	Liver
46	chr6:56440200-56445200	Strong transcription	Fetal Intestine Large	intestine
47	chr6:56440200-56445200	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:56440600-56444600	Strong transcription	Left Ventricle	heart
49	chr6:56440600-56445000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:56440800-56444800	Strong transcription	Fetal Lung	lung

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