Variant report

Variant	rs4272222
Chromosome Location	chr6:53749674-53749675
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10498795	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12196155	0.81[AMR][1000 genomes];0.85[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];0.91[EUR][1000 genomes]
rs16884427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473599	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2473601	0.86[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];0.89[EUR][1000 genomes]
rs2494089	0.86[EUR][1000 genomes]
rs2494090	0.87[EUR][1000 genomes]
rs2494091	0.84[EUR][1000 genomes]
rs2745460	0.87[EUR][1000 genomes]
rs2820217	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077760	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4276504	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4380749	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4397225	0.88[AMR][1000 genomes];0.87[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];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4580851	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6905927	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6908101	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6925165	0.88[AMR][1000 genomes];0.87[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];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7752696	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9463996	0.80[YRI][hapmap]
rs9464005	0.83[AMR][1000 genomes];0.86[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];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	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
rs4272222	FBXO9	cis	parietal	SCAN
rs4272222	C6orf142	cis	cerebellum	SCAN
rs4272222	LRRC1	cis	parietal	SCAN
rs4272222	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53727600-53751800	Weak transcription	Thymus	Thymus
3	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
4	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
5	chr6:53735000-53751800	Weak transcription	Gastric	stomach
6	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
7	chr6:53736200-53751400	Weak transcription	Brain Substantia Nigra	brain
8	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
9	chr6:53739000-53753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:53739000-53753600	Weak transcription	NHEK	skin
11	chr6:53739000-53767800	Weak transcription	Ovary	ovary
12	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
13	chr6:53740000-53750600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:53740000-53752400	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:53740000-53755200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:53740400-53754000	Weak transcription	HSMM	muscle
17	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
20	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
21	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
24	chr6:53744200-53752200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
26	chr6:53744800-53752200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:53744800-53760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:53745400-53760600	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:53746200-53757200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:53746200-53758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:53746400-53758600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:53746800-53762000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:53747000-53753600	Weak transcription	HMEC	breast
37	chr6:53747400-53751600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
39	chr6:53748000-53750600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:53748000-53750600	Strong transcription	HepG2	liver
41	chr6:53748200-53750000	Strong transcription	Dnd41	blood
42	chr6:53748400-53752400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:53748800-53754600	Weak transcription	HSMMtube	muscle
44	chr6:53749000-53761800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:53749200-53751600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:53749200-53751600	Weak transcription	Fetal Thymus	thymus
47	chr6:53749200-53763600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:53749200-53765800	Weak transcription	Primary T cells from cord blood	blood
49	chr6:53749400-53762600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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