Variant report

Variant	rs2820217
Chromosome Location	chr6:53779841-53779842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53658853..53661753-chr6:53777848..53780976,4	MCF-7	breast:
2	chr6:53778649..53781585-chr6:53788522..53790145,2	MCF-7	breast:
3	chr6:53774348..53776830-chr6:53777789..53780459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10498795	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12196155	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1543356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16884427	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473599	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2473601	0.88[EUR][1000 genomes]
rs2473603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494087	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2494089	0.88[EUR][1000 genomes]
rs2494090	0.89[EUR][1000 genomes]
rs2494091	0.87[EUR][1000 genomes]
rs2745460	0.89[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077760	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4272222	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276504	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4380749	0.84[EUR][1000 genomes]
rs4397225	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4476827	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4580851	0.84[EUR][1000 genomes]
rs6903532	0.80[EUR][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6908101	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6925165	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs761135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382261	0.81[EUR][1000 genomes]
rs9382262	0.81[EUR][1000 genomes]
rs9463996	1.00[YRI][hapmap]
rs9464005	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9474672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474680	0.83[AFR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2820217	FBXO9	cis	parietal	SCAN
rs2820217	C6orf142	cis	cerebellum	SCAN
rs2820217	COL21A1	cis	cerebellum	SCAN
rs2820217	LRRC1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
4	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
5	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
8	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
9	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
11	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:53761400-53787400	Weak transcription	HMEC	breast
14	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
16	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
19	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
22	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:53769800-53784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:53769800-53784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:53770000-53781800	Weak transcription	HSMM	muscle
29	chr6:53770000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:53770600-53787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:53771200-53785000	Weak transcription	Left Ventricle	heart
33	chr6:53772000-53784200	Weak transcription	Colonic Mucosa	Colon
34	chr6:53772000-53784400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:53772000-53787600	Weak transcription	Pancreas	Pancrea
36	chr6:53772000-53803000	Weak transcription	Lung	lung
37	chr6:53772800-53783800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:53775800-53781200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53776000-53786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:53776200-53786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:53776400-53786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:53776600-53785200	Weak transcription	Ovary	ovary
44	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
46	chr6:53777000-53781600	Weak transcription	Brain Angular Gyrus	brain
47	chr6:53777600-53790600	Strong transcription	Fetal Thymus	thymus
48	chr6:53778000-53781000	Weak transcription	Brain Anterior Caudate	brain
49	chr6:53778000-53781200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:53778000-53787800	Strong transcription	Dnd41	blood

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