Variant report

Variant	rs6537790
Chromosome Location	chr1:114095208-114095209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10858001	0.86[YRI][hapmap]
rs10858002	0.86[YRI][hapmap]
rs11102651	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs1217216	0.91[ASN][1000 genomes]
rs1217222	0.90[ASN][1000 genomes]
rs1217225	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.91[ASN][1000 genomes]
rs1217231	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1343629	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418957	0.81[YRI][hapmap]
rs17508449	0.80[CHD][hapmap]
rs35390985	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4259646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704188	0.81[YRI][hapmap]
rs7511816	0.82[ASN][1000 genomes]
rs7514649	0.80[CHD][hapmap]
rs7522138	0.84[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7554019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv947128	chr1:114088844-114122533	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6537790	MAGI3	cis	cerebellum	SCAN
rs6537790	PHTF1	cis	cerebellum	SCAN
rs6537790	DCLRE1B	cis	cerebellum	SCAN
rs6537790	BCL2L15	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
2	chr1:114082600-114100400	Weak transcription	Fetal Kidney	kidney
3	chr1:114083200-114099800	Weak transcription	Pancreas	Pancrea
4	chr1:114083400-114100000	Weak transcription	Ovary	ovary
5	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:114084800-114095600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:114085600-114101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:114088200-114102000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:114088600-114099600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:114088600-114101000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:114088600-114109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:114090400-114099800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:114091000-114099800	Weak transcription	Left Ventricle	heart
14	chr1:114091200-114101800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:114092000-114099600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:114092200-114099200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:114092400-114097200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:114092400-114099600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:114092400-114101600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:114093200-114096200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:114093400-114099800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:114093800-114095400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:114094000-114095600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:114094000-114099600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:114094000-114104600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:114094200-114097200	Weak transcription	Small Intestine	intestine
27	chr1:114094200-114099800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:114094200-114100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:114094400-114099600	Weak transcription	Fetal Lung	lung
30	chr1:114094400-114099800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:114094400-114099800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:114094600-114095400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:114094600-114095600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:114094600-114095600	Enhancers	Osteobl	bone
35	chr1:114094800-114099800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:114094800-114099800	Weak transcription	Lung	lung
37	chr1:114094800-114103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:114094800-114138400	Weak transcription	NHDF-Ad	bronchial
39	chr1:114095000-114095400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:114095000-114095400	Enhancers	HSMM	muscle
41	chr1:114095000-114095600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:114095000-114102200	Weak transcription	Placenta	Placenta
43	chr1:114095200-114095600	Strong transcription	Liver	Liver
44	chr1:114095200-114096400	Strong transcription	Fetal Intestine Large	intestine

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