Variant report

Variant	rs4380749
Chromosome Location	chr6:53693655-53693656
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10498795	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs16884427	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17748452	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2473599	0.80[EUR][1000 genomes]
rs2473603	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2494087	0.83[AMR][1000 genomes]
rs2820217	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3000998	0.85[CHB][hapmap]
rs3799261	1.00[JPT][hapmap]
rs4077760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[EUR][1000 genomes]
rs4131378	0.83[EUR][1000 genomes]
rs4272222	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4397225	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476827	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919924	0.86[EUR][1000 genomes]
rs6925165	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7752696	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474672	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4380749	C6orf142	cis	cerebellum	SCAN
rs4380749	FBXO9	cis	parietal	SCAN
rs4380749	TFAP2D	cis	cerebellum	SCAN
rs4380749	LRRC1	cis	parietal	SCAN
rs4380749	COL21A1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
7	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
10	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
11	chr6:53689600-53694400	Enhancers	HepG2	liver
12	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:53689800-53694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:53689800-53695000	Enhancers	HMEC	breast
15	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
17	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
19	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
20	chr6:53690200-53695600	Enhancers	NHEK	skin
21	chr6:53690400-53697200	Enhancers	Brain Anterior Caudate	brain
22	chr6:53690800-53695200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:53691200-53697800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:53691400-53695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:53691400-53697400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:53691800-53695200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr6:53692000-53693800	Enhancers	Brain Angular Gyrus	brain
28	chr6:53692000-53694400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:53692000-53696000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:53692200-53694000	Enhancers	Fetal Thymus	thymus
31	chr6:53692200-53694000	Enhancers	Right Atrium	heart
32	chr6:53692400-53694000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:53692400-53694000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:53692400-53694400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:53692400-53695000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:53692400-53695600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:53692400-53696600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr6:53692400-53697800	Weak transcription	Brain Germinal Matrix	brain
39	chr6:53692600-53694200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr6:53692600-53694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:53692600-53702600	Weak transcription	Aorta	Aorta
42	chr6:53692800-53693800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:53692800-53694200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:53693000-53693800	Enhancers	Colonic Mucosa	Colon
45	chr6:53693000-53695600	Enhancers	Stomach Smooth Muscle	stomach
46	chr6:53693000-53696400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:53693200-53694600	Weak transcription	Hela-S3	cervix
48	chr6:53693200-53695000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr6:53693400-53694200	Weak transcription	HUVEC	blood vessel
50	chr6:53693400-53694400	Weak transcription	H1 Cell Line	embryonic stem cell

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