Variant report

Variant	rs6425482
Chromosome Location	chr1:171882807-171882808
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10436867	0.86[CHB][hapmap]
rs10737340	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798742	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11579330	0.86[CHB][hapmap]
rs12025368	0.86[CHB][hapmap]
rs2093183	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2145381	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2145382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2180746	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2901603	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520188	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7538839	0.86[CHB][hapmap]
rs7547770	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551737	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6425482	BRP44	cis	parietal	SCAN
rs6425482	FMO9P	cis	cerebellum	SCAN
rs6425482	MPZL1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171868800-171884000	Weak transcription	Fetal Lung	lung
2	chr1:171868800-171885000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:171872200-171883000	Weak transcription	Lung	lung
4	chr1:171879800-171908000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:171880000-171883800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:171880200-171883800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:171880400-171885600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:171880800-171884000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:171881000-171885400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:171881000-171886800	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:171881200-171883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:171881200-171883000	Weak transcription	Psoas Muscle	Psoas
13	chr1:171881400-171883200	Flanking Active TSS	A549	lung
14	chr1:171881600-171883000	Enhancers	Brain Anterior Caudate	brain
15	chr1:171881600-171883000	Enhancers	Stomach Mucosa	stomach
16	chr1:171881800-171883200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:171881800-171883200	Enhancers	Brain Substantia Nigra	brain
18	chr1:171882000-171883000	Enhancers	HSMMtube	muscle
19	chr1:171882000-171883200	Enhancers	Hela-S3	cervix
20	chr1:171882000-171883400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:171882000-171884600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:171882000-171889400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:171882200-171883000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr1:171882200-171883200	Enhancers	HUVEC	blood vessel
25	chr1:171882400-171883000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:171882400-171883200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:171882400-171885200	Enhancers	HMEC	breast
28	chr1:171882400-171886000	Enhancers	NHEK	skin
29	chr1:171882600-171883000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:171882600-171883000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:171882600-171883000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:171882600-171883000	Enhancers	Adipose Nuclei	Adipose
33	chr1:171882600-171883000	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr1:171882600-171883000	Enhancers	HSMM	muscle
35	chr1:171882600-171883200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:171882600-171883200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:171882600-171883200	Enhancers	Brain Angular Gyrus	brain
38	chr1:171882600-171883400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:171882600-171884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:171882800-171883200	Enhancers	Rectal Mucosa Donor 31	rectum

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