Variant report

Variant	rs9370544
Chromosome Location	chr6:56476023-56476024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56474701..56476626-chr6:56477322..56479579,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10484858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11751914	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11758339	1.00[ASW][hapmap]
rs11759493	1.00[ASW][hapmap]
rs11969402	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12195236	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12200301	0.91[ASN][1000 genomes]
rs13194995	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13209548	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16888055	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1884284	0.90[GIH][hapmap]
rs1884285	0.94[JPT][hapmap]
rs1884286	0.90[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs2024751	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2230862	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4712135	0.81[EUR][1000 genomes]
rs4712136	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4712137	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4712138	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715630	1.00[ASW][hapmap]
rs4715635	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs636389	1.00[ASW][hapmap]
rs6459166	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6911502	1.00[ASW][hapmap]
rs6919941	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6921099	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6929091	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7741295	1.00[ASW][hapmap]
rs7747060	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772239	0.85[ASN][1000 genomes]
rs9296848	0.87[ASW][hapmap]
rs9349831	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349835	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349836	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357923	0.93[JPT][hapmap]
rs9357927	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9367689	0.90[GIH][hapmap];0.94[JPT][hapmap]
rs9367690	0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370538	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9370539	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9370540	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9370541	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9370542	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs9370543	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9382645	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382650	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9382652	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9382653	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9382654	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382655	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9382656	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9382658	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382659	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9396222	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9396224	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9396225	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396228	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9689355	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9370544	BEND6	cis	cerebellum	SCAN
rs9370544	BMP5	cis	cerebellum	SCAN

Chromatin state (count:97 , 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	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
3	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
4	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
5	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
6	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:56452800-56489400	Strong transcription	Liver	Liver
9	chr6:56453000-56492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:56453000-56502200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:56453000-56506800	Strong transcription	HSMM	muscle
12	chr6:56453400-56476200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:56455400-56486200	Strong transcription	HSMMtube	muscle
14	chr6:56457200-56478200	Weak transcription	Fetal Heart	heart
15	chr6:56457200-56501200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56458800-56488200	Weak transcription	HepG2	liver
17	chr6:56459000-56496200	Weak transcription	Fetal Kidney	kidney
18	chr6:56459000-56502400	Strong transcription	Osteobl	bone
19	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
20	chr6:56459800-56479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:56460600-56496000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
23	chr6:56460800-56476800	Strong transcription	NHDF-Ad	bronchial
24	chr6:56460800-56489000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:56462000-56476600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:56466600-56480800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:56467200-56480200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:56467400-56480200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:56468000-56481400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:56468200-56481800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:56468800-56480800	Weak transcription	Brain Germinal Matrix	brain
32	chr6:56470600-56502200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:56470800-56502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:56471200-56476400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:56471200-56476600	Strong transcription	NH-A	brain
36	chr6:56471600-56477000	Strong transcription	Brain Anterior Caudate	brain
37	chr6:56472200-56476200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:56473400-56476600	Weak transcription	Fetal Intestine Small	intestine
39	chr6:56473600-56476600	Weak transcription	Fetal Stomach	stomach
40	chr6:56473600-56480600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:56474000-56479800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:56474000-56480600	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:56474000-56480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:56474000-56482800	Weak transcription	Right Ventricle	heart
45	chr6:56474000-56484400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:56474200-56479400	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:56474200-56480400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:56474200-56480400	Weak transcription	Fetal Brain Female	brain
49	chr6:56474200-56480600	Weak transcription	NHEK	skin
50	chr6:56474200-56480800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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